diff --git a/workflows/variant-calling/rna-variant-discovery/.dockstore.yml b/workflows/variant-calling/rna-variant-discovery/.dockstore.yml new file mode 100644 index 0000000000..751bed671d --- /dev/null +++ b/workflows/variant-calling/rna-variant-discovery/.dockstore.yml @@ -0,0 +1,11 @@ +version: 1.2 +workflows: +- name: rna-variant-discovery + subclass: Galaxy + publish: true + primaryDescriptorPath: /RNAvar.ga + testParameterFiles: + - /RNAvar-tests.yml + authors: + - name: "Emre Gülben" + orcid: "https://orcid.org/0009-0009-9085-1055" diff --git a/workflows/variant-calling/rna-variant-discovery/CHANGELOG.md b/workflows/variant-calling/rna-variant-discovery/CHANGELOG.md new file mode 100644 index 0000000000..99131a2aab --- /dev/null +++ b/workflows/variant-calling/rna-variant-discovery/CHANGELOG.md @@ -0,0 +1,5 @@ +# Changelog + +## [0.1] - 2026-03-27 + +- First release. \ No newline at end of file diff --git a/workflows/variant-calling/rna-variant-discovery/README.md b/workflows/variant-calling/rna-variant-discovery/README.md new file mode 100644 index 0000000000..51dd90c049 --- /dev/null +++ b/workflows/variant-calling/rna-variant-discovery/README.md @@ -0,0 +1,37 @@ +# RNA-seq Variant Discovery (RNAvar) + +This workflow is a faithful reimplementation of the [nf-core/rnavar](https://nf-co.re/rnavar) pipeline for the Galaxy ecosystem. It handles the transition from raw reads to annotated variants using industry-standard tools and follows the established best practices for RNA-seq variant discovery. + +## Workflow Logic +1. **Alignment:** **STAR** in 2-pass mode for high-accuracy splice-aware mapping. +2. **Preprocessing:** **MarkDuplicates** and **GATK4 SplitNCigarReads** to prepare the BAM for variant calling by splitting reads into exon segments. +3. **Recalibration:** **GATK4 BaseRecalibrator** (BQSR) using known polymorphic sites to adjust base quality scores. +4. **Variant Calling:** **GATK4 HaplotypeCaller** with parameters specifically tuned for RNA-seq (e.g., ignoring soft-clipped bases). +5. **Filtering:** **bcftools filter** applying hard filters (`FS > 30.0`, `QD < 2.0`) to reduce false positives. +6. **Annotation:** Functional annotation of variants using **SnpEff** against a selected local database. + +## Inputs +* **Forward Reads (R1)**: Fastq sequencing reads (forward). Supports gzipped (`.gz`) files. +* **Reverse Reads (R2)**: Fastq sequencing reads (reverse). Supports gzipped (`.gz`) files. +* **Reference Genome**: FASTA file of the reference genome (e.g., hg38). +* **Genome Annotation**: GFF3 file containing gene models for splice-aware alignment. +* **Known Variants (dbSNP)**: VCF file of known polymorphisms for base quality score recalibration. +* **Known Indels**: VCF file of known insertions and deletions for base quality score recalibration. +* **SnpEff Genome Version**: The name of the locally installed SnpEff database (e.g., hg38). +* **Variant Exclusion Filter**: A bcftools-style expression for hard-filtering variants (default: FS > 30.0 || QD < 2.0). +* **STAR Genome Overhang**: Sequence length around junctions for STAR indexing. Set to (Read Length - 1). For example, use 99 for 100bp reads. + +## Outputs +* **Final Annotated Variants**: VCF file containing discovered variants with functional annotations (impact, effect, gene names) from SnpEff. +* **MultiQC Quality Report**: An HTML report aggregating quality metrics from alignment and preprocessing steps. + +## Testing and Parity +The workflow is validated against a targeted subset of human RNA-seq data on chromosome 22, sourced from the [nf-core/rnavar test dataset](https://github.com/nf-core/test-datasets/tree/rnavar). It achieves technical parity with the reference discovery engine, identifying 54 high-confidence variants. + +## Limitations +Compared to the full [nf-core/rnavar (v1.2.3)](https://nf-co.re/rnavar/1.2.3/docs/usage/) implementation, this Galaxy workflow currently has the following limitations: +* **Sample Handling:** Does not support CSV sample sheets; inputs must be provided as individual datasets or collections. +* **Modularity:** Base recalibration (BQSR) and variant filtering are mandatory steps, whereas they are optional in the original pipeline. +* **Preprocessing:** No current support for UMI-Tools-based deduplication or optional read trimming. +* **Annotation:** Variant annotation is restricted to SnpEff; support for other alternatives is not yet implemented. +* **Performance:** The `GATK4 SplitNCigarReads` step is not parallelized, which may impact runtime on very large datasets compared to the Nextflow execution model. \ No newline at end of file diff --git a/workflows/variant-calling/rna-variant-discovery/RNAvar-tests.yml b/workflows/variant-calling/rna-variant-discovery/RNAvar-tests.yml new file mode 100644 index 0000000000..8a97ff881d --- /dev/null +++ b/workflows/variant-calling/rna-variant-discovery/RNAvar-tests.yml @@ -0,0 +1,46 @@ +- doc: Test outline for RNAvar + job: + "Forward Reads (R1)": + class: File + path: test-data/test_rnaseq_1.fastq.gz + filetype: fastqsanger.gz + "Reverse Reads (R2)": + class: File + path: test-data/test_rnaseq_2.fastq.gz + filetype: fastqsanger.gz + "Reference Genome": + class: File + path: test-data/genome.fasta + filetype: fasta + "Genome Annotation": + class: File + path: test-data/genome.gff3 + filetype: gff3 + "Known Variants (dbSNP)": + class: File + path: test-data/dbsnp_146.hg38.vcf + filetype: vcf + "Known Indels": + class: File + path: test-data/mills_and_1000G.indels.vcf + filetype: vcf + "SnpEff Genome Version": hg38 + "Variant Exclusion Filter": "FS > 30.0 || QD < 2.0" + "STAR Genome Overhang": 14 + outputs: + "Final Annotated Variants": + asserts: + # Expected variants: 54 | VCF Header lines: 36 | Total: 90. + - has_n_lines: + n: 90 + # Verify the content is scientifically correct by checking for + # the presence of the target chromosome string. + - has_text: + text: "chr22" + # Ensure SnpEff successfully added functional annotations + - has_text: + text: "ANN=" + "MultiQC Quality Report": + asserts: + - has_text: + text: "MultiQC" diff --git a/workflows/variant-calling/rna-variant-discovery/RNAvar.ga b/workflows/variant-calling/rna-variant-discovery/RNAvar.ga new file mode 100644 index 0000000000..f9cd780a65 --- /dev/null +++ b/workflows/variant-calling/rna-variant-discovery/RNAvar.ga @@ -0,0 +1,972 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "This workflow performs RNA-seq variant discovery using RNA-seq reads, a reference genome, and known variants as inputs to generate high-confidence variant calls with STAR alignment and GATK-based calling.", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0009-0009-9085-1055", + "name": "Emre Gülben" + } + ], + "format-version": "0.1", + "license": "MIT", + "release": "0.1", + "name": "RNA-seq Variant Discovery", + "readme": "# RNA-seq Variant Discovery (RNAvar)\n\nThis workflow is a faithful reimplementation of the [nf-core/rnavar](https://nf-co.re/rnavar) pipeline for the Galaxy ecosystem. It handles the transition from raw reads to annotated variants using industry-standard tools and follows the established best practices for RNA-seq variant discovery.\n\n## Workflow Logic\n1. **Alignment:** **STAR** in 2-pass mode for high-accuracy splice-aware mapping.\n2. **Preprocessing:** **MarkDuplicates** and **GATK4 SplitNCigarReads** to prepare the BAM for variant calling by splitting reads into exon segments.\n3. **Recalibration:** **GATK4 BaseRecalibrator** (BQSR) using known polymorphic sites to adjust base quality scores.\n4. **Variant Calling:** **GATK4 HaplotypeCaller** with parameters specifically tuned for RNA-seq (e.g., ignoring soft-clipped bases).\n5. **Filtering:** **bcftools filter** applying hard filters (`FS > 30.0`, `QD < 2.0`) to reduce false positives.\n6. **Annotation:** Functional annotation of variants using **SnpEff** against a selected local database.\n\n## Inputs\n* **Forward Reads (R1)**: Fastq sequencing reads (forward). Supports gzipped (`.gz`) files.\n* **Reverse Reads (R2)**: Fastq sequencing reads (reverse). Supports gzipped (`.gz`) files.\n* **Reference Genome**: FASTA file of the reference genome (e.g., hg38).\n* **Genome Annotation**: GFF3 file containing gene models for splice-aware alignment.\n* **Known Variants (dbSNP)**: VCF file of known polymorphisms for base quality score recalibration.\n* **Known Indels**: VCF file of known insertions and deletions for base quality score recalibration.\n* **SnpEff Genome Version**: The name of the locally installed SnpEff database (e.g., hg38).\n* **Variant Exclusion Filter**: A bcftools-style expression for hard-filtering variants (default: FS > 30.0 || QD < 2.0).\n* **STAR Genome Overhang**: Sequence length around junctions for STAR indexing. Set to (Read Length - 1). For example, use 99 for 100bp reads.\n\n## Outputs\n* **Final Annotated Variants**: VCF file containing discovered variants with functional annotations (impact, effect, gene names) from SnpEff.\n* **MultiQC Quality Report**: An HTML report aggregating quality metrics from alignment and preprocessing steps.\n\n## Testing and Parity\nThe workflow is validated against a targeted subset of human RNA-seq data on chromosome 22, sourced from the [nf-core/rnavar test dataset](https://github.com/nf-core/test-datasets/tree/rnavar). It achieves technical parity with the reference discovery engine, identifying 54 high-confidence variants.\n\n## Limitations\nCompared to the full [nf-core/rnavar (v1.2.3)](https://nf-co.re/rnavar/1.2.3/docs/usage/) implementation, this Galaxy workflow currently has the following limitations:\n* **Sample Handling:** Does not support CSV sample sheets; inputs must be provided as individual datasets or collections.\n* **Modularity:** Base recalibration (BQSR) and variant filtering are mandatory steps, whereas they are optional in the original pipeline.\n* **Preprocessing:** No current support for UMI-Tools-based deduplication or optional read trimming.\n* **Annotation:** Variant annotation is restricted to SnpEff; support for other alternatives is not yet implemented.\n* **Performance:** The `GATK4 SplitNCigarReads` step is not parallelized, which may impact runtime on very large datasets compared to the Nextflow execution model.", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "Enter the bcftools expression to filter out variants. 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+##phasing=partial +##variationPropertyDocumentationUrl=ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO=SubSNP->Batch.link_out"> +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO=5% minor allele frequency in each and all populations"> +##INFO=5% minor allele frequency in 1+ populations"> +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##INFO= +##INFO== 1% and for which 2 or more founders contribute to that minor allele frequency."> +##contig= +##bcftools_filterVersion=1.9+htslib-1.9 +##bcftools_filterCommand=filter -r chr22:16570000-16610000 dbsnp_146.hg38.chr22.vcf.gz; Date=Thu Mar 25 23:46:27 2021 +##bcftools_viewVersion=1.12+htslib-1.12 +##bcftools_viewCommand=view -O z -o dbsnp_146.hg38.ROI.vcf.gz dbsnp_146.hg38.ROI.vcf; Date=Mon Jun 14 15:19:50 2021 +##bcftools_viewCommand=view -Oz -o dbsnp_146.hg38.vcf.gz dbsnp_146.hg38.vcf; Date=Tue Jun 15 21:54:02 2021 +#CHROM POS ID REF ALT QUAL FILTER INFO +chr22 66 rs568512106 A G . PASS RS=568512106;RSPOS=16570065;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=0 +chr22 67 rs371364157 A G . PASS RS=371364157;RSPOS=16570066;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 68 rs536054182 A C . PASS RS=536054182;RSPOS=16570067;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=0 +chr22 91 rs149338188 ACATT A . PASS RS=149338188;RSPOS=16570091;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x05000000000515003e000200;WGT=1;VC=DIV;ASP;VLD;G5;KGPhase1;KGPhase3;CAF=0.8083,0.1917;COMMON=1 +chr22 91 rs75245162 ACATT A . PASS RS=75245162;RSPOS=16570093;dbSNPBuildID=131;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP;CAF=0.8083,0.1917;COMMON=1 +chr22 96 rs150045226 C T . PASS RS=150045226;RSPOS=16570095;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 103 rs563344083 TC T . PASS RS=563344083;RSPOS=16570103;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.997,0.002995;COMMON=1 +chr22 140 rs370473918 T C . PASS RS=370473918;RSPOS=16570139;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 177 rs553984036 C A . PASS RS=553984036;RSPOS=16570176;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 208 rs565829750 T C . PASS RS=565829750;RSPOS=16570207;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 212 rs530869804 T C . PASS RS=530869804;RSPOS=16570211;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000026000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 268 rs532520425 T C . PASS RS=532520425;RSPOS=16570267;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 295 rs112756104 G A . PASS RS=112756104;RSPOS=16570294;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 326 rs576397961 T C . PASS RS=576397961;RSPOS=16570325;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 389 rs543323049 G A . PASS RS=543323049;RSPOS=16570388;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 424 rs544340165 C T . PASS RS=544340165;RSPOS=16570423;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 435 rs555644669 A G . PASS RS=555644669;RSPOS=16570434;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 441 rs573894201 C T . PASS RS=573894201;RSPOS=16570440;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 442 rs541225026 G A . PASS RS=541225026;RSPOS=16570441;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 474 rs559615885 A G . PASS RS=559615885;RSPOS=16570473;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=1,0;COMMON=0 +chr22 479 rs193193184 G T . PASS RS=193193184;RSPOS=16570478;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9956,0.004393;COMMON=1 +chr22 529 rs545142889 A G . PASS RS=545142889;RSPOS=16570528;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9968,0.003195;COMMON=1 +chr22 530 rs111578332 T G . PASS RS=111578332;RSPOS=16570529;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050000000005150536000100;WGT=1;VC=SNV;ASP;VLD;G5;HD;GNO;KGPhase1;KGPhase3;CAF=0.8948,0.1052;COMMON=1 +chr22 540 rs183457442 G A . PASS RS=183457442;RSPOS=16570539;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9986,0.001398;COMMON=1 +chr22 551 rs187203379 T G . PASS RS=187203379;RSPOS=16570550;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.991,0.008986;COMMON=1 +chr22 572 rs769857327 A G . PASS RS=769857327;RSPOS=16570571;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 621 rs192590295 C T . PASS RS=192590295;RSPOS=16570620;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9958,0.004193;COMMON=1 +chr22 622 rs529587488 G A . PASS RS=529587488;RSPOS=16570621;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9992,0.0007987;COMMON=1 +chr22 649 rs184576184 G A . PASS RS=184576184;RSPOS=16570648;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 654 rs565967130 T C . PASS RS=565967130;RSPOS=16570653;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=1 +chr22 676 rs188283274 C T . PASS RS=188283274;RSPOS=16570675;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000014000100;WGT=1;VC=SNV;ASP;KGPhase1 +chr22 694 rs769415646 A G . PASS RS=769415646;RSPOS=16570693;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 769 rs192231712 T C . PASS RS=192231712;RSPOS=16570768;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.999,0.0009984;COMMON=1 +chr22 784 rs557851384 A G . PASS RS=557851384;RSPOS=16570783;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=1 +chr22 789 rs569912450 G A . PASS RS=569912450;RSPOS=16570788;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 830 rs537445217 C T . PASS RS=537445217;RSPOS=16570829;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 840 rs555525590 C A . PASS RS=555525590;RSPOS=16570839;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9986,0.001398;COMMON=1 +chr22 860 rs773160421 C T . PASS RS=773160421;RSPOS=16570859;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 861 rs573858529 G T . PASS RS=573858529;RSPOS=16570860;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 886 rs4819755 T G . PASS RS=4819755;RSPOS=16570885;dbSNPBuildID=111;SSR=0;SAO=0;VP=0x050100000005170136000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5A;G5;GNO;KGPhase1;KGPhase3;CAF=0.7618,0.2382;COMMON=1 +chr22 894 rs553173056 C T . PASS RS=553173056;RSPOS=16570893;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 902 rs770956124 T C . PASS RS=770956124;RSPOS=16570901;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 945 rs774479206 G A . PASS RS=774479206;RSPOS=16570944;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 958 rs530857600 TGGGA T . PASS RS=530857600;RSPOS=16570958;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.997,0.002995;COMMON=1 +chr22 963 rs556944478 G A . PASS RS=556944478;RSPOS=16570962;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 1038 rs185050097 A G . PASS RS=185050097;RSPOS=16571037;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9994,0.000599;COMMON=0 +chr22 1089 rs372316282 A T . PASS RS=372316282;RSPOS=16571088;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1150 rs374101703 C T . PASS RS=374101703;RSPOS=16571149;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1223 rs563404543 A G . PASS RS=563404543;RSPOS=16571222;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 1234 rs7511075 G A . PASS RS=7511075;RSPOS=16571233;dbSNPBuildID=116;SSR=0;SAO=0;VP=0x05010000000517013e000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5A;G5;GNO;KGPhase1;KGPhase3;CAF=0.5689,0.4311;COMMON=1 +chr22 1240 rs143325886 C T . PASS RS=143325886;RSPOS=16571239;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 1330 rs62228716 G C . PASS RS=62228716;RSPOS=16571329;dbSNPBuildID=129;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1342 rs147546942 T C . PASS RS=147546942;RSPOS=16571341;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040436000100;WGT=1;VC=SNV;ASP;VLD;HD;KGPhase1;KGPhase3;CAF=0.9912,0.008786;COMMON=1 +chr22 1354 rs62228717 C T . PASS RS=62228717;RSPOS=16571353;dbSNPBuildID=129;SSR=0;SAO=0;VP=0x050000000005000036000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 1363 rs141963076 T G . PASS RS=141963076;RSPOS=16571362;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9912,0.008786;COMMON=1 +chr22 1386 rs553056971 T G . PASS RS=553056971;RSPOS=16571385;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1389 rs573096908 A G . PASS RS=573096908;RSPOS=16571388;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1472 rs374045261 C CA . PASS RS=374045261;RSPOS=16571471;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 1472 rs564455755 C CA . PASS RS=564455755;RSPOS=16571472;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3 +chr22 1472 rs552532699 CA C . PASS RS=552532699;RSPOS=16571472;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3 +chr22 1479 rs770738743 AT A . PASS RS=770738743;RSPOS=16571479;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 1491 rs189614340 G A . PASS RS=189614340;RSPOS=16571490;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9994,0.000599;COMMON=0 +chr22 1538 rs367891073 T C . PASS RS=367891073;RSPOS=16571537;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000026000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 1578 rs558771386 G A . PASS RS=558771386;RSPOS=16571577;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1580 rs551730041 C T . PASS RS=551730041;RSPOS=16571579;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=0 +chr22 1769 rs570132427 T A . PASS RS=570132427;RSPOS=16571768;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 1776 rs774319494 G GT . PASS RS=774319494;RSPOS=16571775;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 1838 rs575524142 T C . PASS RS=575524142;RSPOS=16571837;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1852 rs372134544 G C . PASS RS=372134544;RSPOS=16571851;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1874 rs759304288 TAA T . PASS RS=759304288;RSPOS=16571874;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 1880 rs774478364 C T . PASS RS=774478364;RSPOS=16571879;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1884 rs375719184 C T . PASS RS=375719184;RSPOS=16571883;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1885 rs774936782 A C . PASS RS=774936782;RSPOS=16571884;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1914 rs181103243 A G . PASS RS=181103243;RSPOS=16571913;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 1934 rs186856684 T G . PASS RS=186856684;RSPOS=16571933;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9956,0.004393;COMMON=1 +chr22 1941 rs367939592 G A . PASS RS=367939592;RSPOS=16571940;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 1947 rs752293154 GC G . PASS RS=752293154;RSPOS=16571947;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 1974 rs567681764 C T . PASS RS=567681764;RSPOS=16571973;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 1982 rs7287620 A G . PASS RS=7287620;RSPOS=16571981;dbSNPBuildID=116;SSR=0;SAO=0;VP=0x050000000005150036000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase1;KGPhase3;CAF=0.888,0.112;COMMON=1 +chr22 2060 rs182041500 G A . PASS RS=182041500;RSPOS=16572059;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005140036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9864,0.01358;COMMON=1 +chr22 2061 rs577869981 G C . PASS RS=577869981;RSPOS=16572060;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=1 +chr22 2095 rs538825365 A G . PASS RS=538825365;RSPOS=16572094;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=1 +chr22 2124 rs765538760 G A . PASS RS=765538760;RSPOS=16572123;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 2143 rs150741494 T C . PASS RS=150741494;RSPOS=16572142;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9988,0.001198;COMMON=1 +chr22 2151 rs760358365 AGG A . PASS RS=760358365;RSPOS=16572151;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 2175 rs775563753 T G . PASS RS=775563753;RSPOS=16572174;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 2188 rs186375979 C A . PASS RS=186375979;RSPOS=16572187;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9956,0.004393;COMMON=1 +chr22 2241 rs371919832 T C . PASS RS=371919832;RSPOS=16572240;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 2258 rs190043949 G T . PASS RS=190043949;RSPOS=16572257;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 2260 rs182530734 A G . PASS RS=182530734;RSPOS=16572259;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 2283 rs139102553 A G . PASS RS=139102553;RSPOS=16572282;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.991,0.008986;COMMON=1 +chr22 2298 rs541279542 T C . PASS RS=541279542;RSPOS=16572297;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 2302 rs559610819 T A . PASS RS=559610819;RSPOS=16572301;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 2392 rs760684584 G C . PASS RS=760684584;RSPOS=16572391;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 2504 rs561377371 C T . PASS RS=561377371;RSPOS=16572503;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9992,0.0007987;COMMON=0 +chr22 2509 rs185915802 G A . PASS RS=185915802;RSPOS=16572508;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000036000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 2563 rs191182702 G C . PASS RS=191182702;RSPOS=16572562;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9978,0.002196;COMMON=1 +chr22 2597 rs531003083 G A . PASS RS=531003083;RSPOS=16572596;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 2598 rs549234886 C G . PASS RS=549234886;RSPOS=16572597;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 2608 rs5747929 T C . PASS RS=5747929;RSPOS=16572607;dbSNPBuildID=114;SSR=0;SAO=0;VP=0x050100000005000136000100;WGT=1;VC=SNV;SLO;ASP;GNO;KGPhase1;KGPhase3;CAF=0,1;COMMON=0 +chr22 2624 rs535027368 A G . PASS RS=535027368;RSPOS=16572623;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 2629 rs183150738 A G . PASS RS=183150738;RSPOS=16572628;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9912,0.008786;COMMON=1 +chr22 2658 rs146425538 G T . PASS RS=146425538;RSPOS=16572657;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005150036000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase1;KGPhase3;CAF=0.9431,0.05691;COMMON=1 +chr22 2688 rs538582494 T A . PASS RS=538582494;RSPOS=16572687;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 2708 rs560184502 G A . PASS RS=560184502;RSPOS=16572707;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 2791 rs557100773 A G . PASS RS=557100773;RSPOS=16572790;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 2812 rs575364526 A G . PASS RS=575364526;RSPOS=16572811;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9992,0.0007987;COMMON=1 +chr22 2816 rs187430919 T C . PASS RS=187430919;RSPOS=16572815;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.991,0.008986;COMMON=1 +chr22 2849 rs139832769 A G . PASS RS=139832769;RSPOS=16572848;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.998,0.001997;COMMON=1 +chr22 2869 rs572464473 T C . PASS RS=572464473;RSPOS=16572868;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3056 rs539841585 T C . PASS RS=539841585;RSPOS=16573055;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3093 rs564567768 A T . PASS RS=564567768;RSPOS=16573092;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3094 rs577902094 G A . PASS RS=577902094;RSPOS=16573093;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3097 rs192021995 T G . PASS RS=192021995;RSPOS=16573096;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9948,0.005192;COMMON=1 +chr22 3121 rs563881667 C T . PASS RS=563881667;RSPOS=16573120;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3131 rs200758269 A G . PASS RS=200758269;RSPOS=16573130;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9988,0.001198;COMMON=1 +chr22 3138 rs17430900 G A . PASS RS=17430900;RSPOS=16573137;dbSNPBuildID=123;SSR=0;SAO=0;VP=0x050000000005040537000100;WGT=1;VC=SNV;ASP;VLD;HD;GNO;KGPhase1;KGPhase3;CAF=0.9964,0.003594;COMMON=1 +chr22 3189 rs561356601 C T . PASS RS=561356601;RSPOS=16573188;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3214 rs4008588 G A . PASS RS=4008588;RSPOS=16573213;dbSNPBuildID=108;SSR=0;SAO=0;VP=0x050000000005150036000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase1;KGPhase3;CAF=0.8624,0.1376;COMMON=1 +chr22 3266 rs4008589 T C . PASS RS=4008589;RSPOS=16573265;dbSNPBuildID=108;SSR=0;SAO=0;VP=0x050100000005000136000100;WGT=1;VC=SNV;SLO;ASP;GNO;KGPhase1;KGPhase3;CAF=0,1;COMMON=0 +chr22 3271 rs187731265 T G . PASS RS=187731265;RSPOS=16573270;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9912,0.008786;COMMON=1 +chr22 3310 rs148872466 A G . PASS RS=148872466;RSPOS=16573309;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9942,0.005791;COMMON=1 +chr22 3312 rs550622682 T A . PASS RS=550622682;RSPOS=16573311;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3330 rs568986459 T A,G . PASS RS=568986459;RSPOS=16573329;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000026000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,.,0.0001997;COMMON=0 +chr22 3335 rs536065537 A T . PASS RS=536065537;RSPOS=16573334;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 3348 rs528563969 ACTTT A . PASS RS=528563969;RSPOS=16573348;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=1 +chr22 3378 rs554390743 C T . PASS RS=554390743;RSPOS=16573377;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3402 rs73159808 T C . PASS RS=73159808;RSPOS=16573401;dbSNPBuildID=130;SSR=0;SAO=0;VP=0x05000000000515003e000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase1;KGPhase3;CAF=0.9649,0.03514;COMMON=1 +chr22 3405 rs547296568 G GT . PASS RS=547296568;RSPOS=16573404;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.9992,0.0007987;COMMON=0 +chr22 3440 rs755635883 C T . PASS RS=755635883;RSPOS=16573439;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 3443 rs143558414 T C . PASS RS=143558414;RSPOS=16573442;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005150036000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase1;KGPhase3;CAF=0.8624,0.1376;COMMON=1 +chr22 3490 rs753441139 TAATC T . PASS RS=753441139;RSPOS=16573490;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 3506 rs558097087 C T . PASS RS=558097087;RSPOS=16573505;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.997,0.002995;COMMON=1 +chr22 3527 rs193214713 A G . PASS RS=193214713;RSPOS=16573526;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3547 rs545638801 C T . PASS RS=545638801;RSPOS=16573546;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 3566 rs557380987 C T . PASS RS=557380987;RSPOS=16573565;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3601 rs575936217 G T . PASS RS=575936217;RSPOS=16573600;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3611 rs542847154 T C . PASS RS=542847154;RSPOS=16573610;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3618 rs561492117 T C . PASS RS=561492117;RSPOS=16573617;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3665 rs749208140 A G . PASS RS=749208140;RSPOS=16573664;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 3688 rs567257926 T C . PASS RS=567257926;RSPOS=16573687;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 3748 rs536226121 C T . PASS RS=536226121;RSPOS=16573747;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 3799 rs528577910 C T . PASS RS=528577910;RSPOS=16573798;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 3831 rs9605903 T C . PASS RS=9605903;RSPOS=16573830;dbSNPBuildID=119;SSR=0;SAO=0;VP=0x050100000005150537000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5;HD;GNO;KGPhase1;KGPhase3;CAF=0.8155,0.1845;COMMON=1 +chr22 3857 rs201647018 G GA . PASS RS=201647018;RSPOS=16573856;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x05000000000504003c000200;WGT=1;VC=DIV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9908,0.009185;COMMON=1 +chr22 3885 rs184363644 G C . PASS RS=184363644;RSPOS=16573884;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 3906 rs73159809 G A . PASS RS=73159809;RSPOS=16573905;dbSNPBuildID=131;SSR=0;SAO=0;VP=0x050000000005150436000100;WGT=1;VC=SNV;ASP;VLD;G5;HD;KGPhase1;KGPhase3;CAF=0.871,0.129;COMMON=1 +chr22 3947 rs780485911 GT G . PASS RS=780485911;RSPOS=16573947;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 3952 rs558765594 G C . PASS RS=558765594;RSPOS=16573951;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.999,0.0009984;COMMON=1 +chr22 3958 rs117062864 T A . PASS RS=117062864;RSPOS=16573957;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050000000005150036000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase1;KGPhase3;CAF=0.9557,0.04433;COMMON=1 +chr22 4025 rs530032056 G A . PASS RS=530032056;RSPOS=16574024;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=0 +chr22 4036 rs373149213 A G . PASS RS=373149213;RSPOS=16574035;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=1 +chr22 4051 rs114810837 G A . PASS RS=114810837;RSPOS=16574050;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.991,0.008986;COMMON=1 +chr22 4058 rs189346500 A G . PASS RS=189346500;RSPOS=16574057;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 4063 rs558236235 A T . PASS RS=558236235;RSPOS=16574062;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4140 rs570389443 C T . PASS RS=570389443;RSPOS=16574139;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4153 rs537434710 C T . PASS RS=537434710;RSPOS=16574152;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4161 rs556173300 A G . PASS RS=556173300;RSPOS=16574160;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4182 rs80316672 A G . PASS RS=80316672;RSPOS=16574181;dbSNPBuildID=131;SSR=0;SAO=0;VP=0x050000000005000102000100;WGT=1;VC=SNV;ASP;GNO +chr22 4185 rs28493915 T A . PASS RS=28493915;RSPOS=16574184;dbSNPBuildID=125;SSR=0;SAO=0;VP=0x050100000005150136000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;CAF=0.8153,0.1847;COMMON=1 +chr22 4187 rs9605904 C T . PASS RS=9605904;RSPOS=16574186;dbSNPBuildID=119;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4228 rs192741164 G A . PASS RS=192741164;RSPOS=16574227;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9974,0.002596;COMMON=1 +chr22 4233 rs184114773 C A . PASS RS=184114773;RSPOS=16574232;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9974,0.002596;COMMON=1 +chr22 4234 rs189189027 T G . PASS RS=189189027;RSPOS=16574233;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9956,0.004393;COMMON=1 +chr22 4239 rs764123100 G A . PASS RS=764123100;RSPOS=16574238;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4290 rs540683950 C A . PASS RS=540683950;RSPOS=16574289;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4309 rs777184757 TG T . PASS RS=777184757;RSPOS=16574309;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 4358 rs745821165 A T . PASS RS=745821165;RSPOS=16574357;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4431 rs565243048 A T . PASS RS=565243048;RSPOS=16574430;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4438 rs577307358 T A . PASS RS=577307358;RSPOS=16574437;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4439 rs771427191 T A . PASS RS=771427191;RSPOS=16574438;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4461 rs775089417 T C . PASS RS=775089417;RSPOS=16574460;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4479 rs112739091 A G . PASS RS=112739091;RSPOS=16574478;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050100000005040136000100;WGT=1;VC=SNV;SLO;ASP;VLD;GNO;KGPhase1;KGPhase3;CAF=0.991,0.008986;COMMON=1 +chr22 4528 rs181598593 G A . PASS RS=181598593;RSPOS=16574527;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4539 rs574796372 A T . PASS RS=574796372;RSPOS=16574538;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4548 rs529913033 A G . PASS RS=529913033;RSPOS=16574547;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4552 rs202173671 A C . PASS RS=202173671;RSPOS=16574551;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x050000000005000026000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4569 rs35893428 G A . PASS RS=35893428;RSPOS=16574568;dbSNPBuildID=126;SSR=0;SAO=0;VP=0x050100000005150136000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;CAF=0.8171,0.1829;COMMON=1 +chr22 4631 rs527496358 A T . PASS RS=527496358;RSPOS=16574630;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4665 rs768267596 C T . PASS RS=768267596;RSPOS=16574664;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4667 rs141594658 C G . PASS RS=141594658;RSPOS=16574666;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9932,0.006789;COMMON=1 +chr22 4680 rs3729688 T G . PASS RS=3729688;RSPOS=16574679;dbSNPBuildID=107;SSR=0;SAO=0;VP=0x050100000005170537000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5A;G5;HD;GNO;KGPhase1;KGPhase3;CAF=0.5725,0.4275;COMMON=1 +chr22 4721 rs758648248 T C . PASS RS=758648248;RSPOS=16574720;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4793 rs763295824 C A . PASS RS=763295824;RSPOS=16574792;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4813 rs368292686 C T . PASS RS=368292686;RSPOS=16574812;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=0 +chr22 4854 rs549494101 G A . PASS RS=549494101;RSPOS=16574853;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4860 rs766799327 C G . PASS RS=766799327;RSPOS=16574859;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4879 rs138348065 A G . PASS RS=138348065;RSPOS=16574878;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040436000100;WGT=1;VC=SNV;ASP;VLD;HD;KGPhase1;KGPhase3;CAF=0.9954,0.004593;COMMON=1 +chr22 4885 rs545889523 G T . PASS RS=545889523;RSPOS=16574884;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 4914 rs761981591 G GAA . PASS RS=761981591;RSPOS=16574913;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 4929 rs5746642 C T . PASS RS=5746642;RSPOS=16574928;dbSNPBuildID=114;SSR=0;SAO=0;VP=0x05010000000517053f000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5A;G5;HD;GNO;KGPhase1;KGPhase3;CAF=0.5719,0.4281;COMMON=1 +chr22 4937 rs186556477 T C . PASS RS=186556477;RSPOS=16574936;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 4946 rs12167960 C G . PASS RS=12167960;RSPOS=16574945;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9948,0.005192;COMMON=1 +chr22 4952 rs5747939 C T . PASS RS=5747939;RSPOS=16574951;dbSNPBuildID=114;SSR=0;SAO=0;VP=0x050100000005170136000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5A;G5;GNO;KGPhase1;KGPhase3;CAF=0.1791,0.8209;COMMON=1 +chr22 4990 rs559151059 T C . PASS RS=559151059;RSPOS=16574989;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 5023 rs777419108 A G . PASS RS=777419108;RSPOS=16575022;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5034 rs753780503 A T . PASS RS=753780503;RSPOS=16575033;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5089 rs147996299 G A . PASS RS=147996299;RSPOS=16575088;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005150036000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase1;KGPhase3;CAF=0.8624,0.1376;COMMON=1 +chr22 5095 rs13056626 C T . PASS RS=13056626;RSPOS=16575094;dbSNPBuildID=121;SSR=0;SAO=0;VP=0x050100000005150136000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;CAF=0.8153,0.1847;COMMON=1 +chr22 5133 rs11089243 T C . PASS RS=11089243;RSPOS=16575132;dbSNPBuildID=120;SSR=0;SAO=0;VP=0x05010000000515053f000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5;HD;GNO;KGPhase1;KGPhase3;CAF=0.9728,0.02716;COMMON=1 +chr22 5149 rs5746643 G A . PASS RS=5746643;RSPOS=16575148;dbSNPBuildID=114;SSR=0;SAO=0;VP=0x050100000005170136000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5A;G5;GNO;KGPhase1;KGPhase3;CAF=0.2843,0.7157;COMMON=1 +chr22 5178 rs35857110 C CT,CTT . PASS RS=35857110;RSPOS=16575177;dbSNPBuildID=126;SSR=0;SAO=0;VP=0x05000000000514002e000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.1382,0.6849,0.1769;COMMON=1 +chr22 5178 rs60487879 C CT,CTT . PASS RS=60487879;RSPOS=16575187;dbSNPBuildID=129;SSR=0;SAO=0;VP=0x050100000005000102000200;WGT=1;VC=DIV;SLO;ASP;GNO;CAF=0.1382,0.6849,0.1769;COMMON=1 +chr22 5206 rs534765664 T C . PASS RS=534765664;RSPOS=16575205;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5208 rs541683410 T C . PASS RS=541683410;RSPOS=16575207;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 5213 rs560008518 C A . PASS RS=560008518;RSPOS=16575212;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 5220 rs546648471 G T . PASS RS=546648471;RSPOS=16575219;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5223 rs190412113 T C . PASS RS=190412113;RSPOS=16575222;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.999,0.0009984;COMMON=1 +chr22 5244 rs145982399 C T . PASS RS=145982399;RSPOS=16575243;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9954,0.004593;COMMON=1 +chr22 5254 rs373176526 T C . PASS RS=373176526;RSPOS=16575253;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5282 rs771719491 C T . PASS RS=771719491;RSPOS=16575281;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5305 rs564338539 G C . PASS RS=564338539;RSPOS=16575304;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 5313 rs531271314 G A . PASS RS=531271314;RSPOS=16575312;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 5361 rs182201242 G A . PASS RS=182201242;RSPOS=16575360;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 5388 rs538782082 C T . PASS RS=538782082;RSPOS=16575387;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 5391 rs5746644 C A . PASS RS=5746644;RSPOS=16575390;dbSNPBuildID=114;SSR=0;SAO=0;VP=0x050100000005150136000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;CAF=0.04153,0.9585;COMMON=1 +chr22 5394 rs745745266 A C . PASS RS=745745266;RSPOS=16575393;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5406 rs768778983 C A . PASS RS=768778983;RSPOS=16575405;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5409 rs5746645 G T . PASS RS=5746645;RSPOS=16575408;dbSNPBuildID=114;SSR=0;SAO=0;VP=0x050100000005170136000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5A;G5;GNO;KGPhase1;KGPhase3;CAF=0.5689,0.4311;COMMON=1 +chr22 5433 rs567167463 A T . PASS RS=567167463;RSPOS=16575432;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.999,0.0009984;COMMON=1 +chr22 5445 rs60800026 G A . PASS RS=60800026;RSPOS=16575444;dbSNPBuildID=129;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5483 rs534532522 G T . PASS RS=534532522;RSPOS=16575482;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 5485 rs558851159 T C . PASS RS=558851159;RSPOS=16575484;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=1 +chr22 5513 rs186033717 T A . PASS RS=186033717;RSPOS=16575512;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 5526 rs5747940 T C . PASS RS=5747940;RSPOS=16575525;dbSNPBuildID=114;SSR=0;SAO=0;VP=0x050100000005170537000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5A;G5;HD;GNO;KGPhase1;KGPhase3;CAF=0.5725,0.4275;COMMON=1 +chr22 5601 rs554862926 A G . PASS RS=554862926;RSPOS=16575600;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000026000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 5628 rs190894336 T C . PASS RS=190894336;RSPOS=16575627;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9984,0.001597;COMMON=1 +chr22 5634 rs574424714 T C . PASS RS=574424714;RSPOS=16575633;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5652 rs541820321 A T . PASS RS=541820321;RSPOS=16575651;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 5654 rs553779897 C T . PASS RS=553779897;RSPOS=16575653;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=1 +chr22 5715 rs571990592 T C . PASS RS=571990592;RSPOS=16575714;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 5745 rs543070521 T C . PASS RS=543070521;RSPOS=16575744;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5763 rs181408756 C G . PASS RS=181408756;RSPOS=16575762;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 5764 rs533813117 G A . PASS RS=533813117;RSPOS=16575763;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5783 rs185379208 C A . PASS RS=185379208;RSPOS=16575782;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.997,0.002995;COMMON=1 +chr22 5815 rs112221049 T A . PASS RS=112221049;RSPOS=16575814;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 5899 rs377356666 T C . PASS RS=377356666;RSPOS=16575898;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9976,0.002396;COMMON=1 +chr22 5951 rs7290826 T C . PASS RS=7290826;RSPOS=16575950;dbSNPBuildID=116;SSR=0;SAO=0;VP=0x050000000005150036000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase1;KGPhase3;CAF=0.9465,0.05351;COMMON=1 +chr22 5959 rs561757883 C T . PASS RS=561757883;RSPOS=16575958;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 6013 rs546287622 G C . PASS RS=546287622;RSPOS=16576012;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6019 rs529043578 C T . PASS RS=529043578;RSPOS=16576018;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9992,0.0007987;COMMON=0 +chr22 6056 rs547394234 T C . PASS RS=547394234;RSPOS=16576055;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 6133 rs190682322 C T . PASS RS=190682322;RSPOS=16576132;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000036000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 6140 rs527963105 A G . PASS RS=527963105;RSPOS=16576139;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=0 +chr22 6195 rs562814139 G A . PASS RS=562814139;RSPOS=16576194;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9954,0.004593;COMMON=1 +chr22 6217 rs570917183 A C . PASS RS=570917183;RSPOS=16576216;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9994,0.000599;COMMON=0 +chr22 6246 rs538427362 A G . PASS RS=538427362;RSPOS=16576245;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 6249 rs5746647 G T . PASS RS=5746647;RSPOS=16576248;dbSNPBuildID=114;SSR=0;SAO=0;VP=0x050128000005150537020100;WGT=1;VC=SNV;PM;PMC;SLO;ASP;VLD;G5;HD;GNO;KGPhase1;KGPhase3;MTP;CAF=0.1002,0.8998;COMMON=1 +chr22 6306 rs561108320 G A . PASS RS=561108320;RSPOS=16576305;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6323 rs746506316 A G . PASS RS=746506316;RSPOS=16576322;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6344 rs576721579 T C . PASS RS=576721579;RSPOS=16576343;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6345 rs760392899 A G . PASS RS=760392899;RSPOS=16576344;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6354 rs768216601 A G . PASS RS=768216601;RSPOS=16576353;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6365 rs142209939 A G . PASS RS=142209939;RSPOS=16576364;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9968,0.003195;COMMON=1 +chr22 6369 rs763783681 A G . PASS RS=763783681;RSPOS=16576368;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6415 rs535589425 T A . PASS RS=535589425;RSPOS=16576414;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 6464 rs182917259 C A . PASS RS=182917259;RSPOS=16576463;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9994,0.000599;COMMON=0 +chr22 6465 rs572128299 C A . PASS RS=572128299;RSPOS=16576464;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 6554 rs569964227 CTG C . PASS RS=569964227;RSPOS=16576554;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.9946,0.005391;COMMON=1 +chr22 6592 rs187214357 G A . PASS RS=187214357;RSPOS=16576591;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.999,0.0009984;COMMON=0 +chr22 6601 rs375246176 C T . PASS RS=375246176;RSPOS=16576600;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6605 rs549655946 G GTT . PASS RS=549655946;RSPOS=16576604;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.995,0.004992;COMMON=1 +chr22 6619 rs144718072 G A . PASS RS=144718072;RSPOS=16576618;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9916,0.008387;COMMON=1 +chr22 6661 rs369850963 G T . PASS RS=369850963;RSPOS=16576660;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9988,0.001198;COMMON=1 +chr22 6683 rs543598345 A G . PASS RS=543598345;RSPOS=16576682;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9972,0.002796;COMMON=1 +chr22 6693 rs373305703 G A . PASS RS=373305703;RSPOS=16576692;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6702 rs116981477 G A . PASS RS=116981477;RSPOS=16576701;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050000000005040436000100;WGT=1;VC=SNV;ASP;VLD;HD;KGPhase1;KGPhase3;CAF=0.9966,0.003395;COMMON=1 +chr22 6708 rs4819760 G A . PASS RS=4819760;RSPOS=16576707;dbSNPBuildID=111;SSR=0;SAO=0;VP=0x050100000005150536000101;WGT=1;VC=SNV;SLO;ASP;VLD;G5;HD;GNO;KGPhase1;KGPhase3;CAF=0.8161,0.1839;COMMON=1 +chr22 6806 rs541149525 A C . PASS RS=541149525;RSPOS=16576805;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 6870 rs548102555 A G . PASS RS=548102555;RSPOS=16576869;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6933 rs112827160 A G . PASS RS=112827160;RSPOS=16576932;dbSNPBuildID=132;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 6965 rs192038831 T A . PASS RS=192038831;RSPOS=16576964;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000036000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 6980 rs532952456 C T . PASS RS=532952456;RSPOS=16576979;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=1 +chr22 7001 rs532101447 G A . PASS RS=532101447;RSPOS=16577000;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 7065 rs200134928 TTC T . PASS RS=200134928;RSPOS=16577065;dbSNPBuildID=137;SSR=0;SAO=0;VP=0x05000000000504003e000200;WGT=1;VC=DIV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9932,0.006789;COMMON=1 +chr22 7108 rs561126676 GA G . PASS RS=561126676;RSPOS=16577108;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 7136 rs771230443 T C . PASS RS=771230443;RSPOS=16577135;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 7202 rs551132913 A C . PASS RS=551132913;RSPOS=16577201;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 7205 rs183918989 G T . PASS RS=183918989;RSPOS=16577204;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.996,0.003994;COMMON=1 +chr22 7246 rs531943188 C G . PASS RS=531943188;RSPOS=16577245;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9992,0.0007987;COMMON=1 +chr22 7260 rs368931956 AT A . PASS RS=368931956;RSPOS=16577260;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005040026000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.996,0.003994;COMMON=1 +chr22 7266 rs187721014 T C . PASS RS=187721014;RSPOS=16577265;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 7275 rs568328713 A T . PASS RS=568328713;RSPOS=16577274;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 7283 rs192651001 T G . PASS RS=192651001;RSPOS=16577282;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 7311 rs553851160 C A . PASS RS=553851160;RSPOS=16577310;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 7357 rs184345485 G A . PASS RS=184345485;RSPOS=16577356;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000014000100;WGT=1;VC=SNV;ASP;KGPhase1 +chr22 7366 rs565694732 G T . PASS RS=565694732;RSPOS=16577365;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 7379 rs141531577 A G . PASS RS=141531577;RSPOS=16577378;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9988,0.001198;COMMON=1 +chr22 7382 rs372504812 T C . PASS RS=372504812;RSPOS=16577381;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 7396 rs557911307 G C . PASS RS=557911307;RSPOS=16577395;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 7491 rs568822821 G A . PASS RS=568822821;RSPOS=16577490;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 7593 rs3732991 T C . PASS RS=3732991;RSPOS=16577592;dbSNPBuildID=114;SSR=0;SAO=0;VP=0x050000000005170036000100;WGT=1;VC=SNV;ASP;VLD;G5A;G5;KGPhase1;KGPhase3;CAF=0.7812,0.2188;COMMON=1 +chr22 7627 rs9618435 C T . PASS RS=9618435;RSPOS=16577626;dbSNPBuildID=119;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 7637 rs148159902 A T . PASS RS=148159902;RSPOS=16577636;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005150036000100;WGT=1;VC=SNV;ASP;VLD;G5;KGPhase1;KGPhase3;CAF=0.9569,0.04313;COMMON=1 +chr22 7666 rs187130993 C T . PASS RS=187130993;RSPOS=16577665;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.993,0.006989;COMMON=1 +chr22 7671 rs4239851 A G . PASS RS=4239851;RSPOS=16577670;dbSNPBuildID=111;SSR=0;SAO=0;VP=0x050100000005150536000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5;HD;GNO;KGPhase1;KGPhase3;CAF=0.08586,0.9141;COMMON=1 +chr22 7706 rs533874338 C T . PASS RS=533874338;RSPOS=16577705;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 7707 rs191635420 G A . PASS RS=191635420;RSPOS=16577706;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.998,0.001997;COMMON=1 +chr22 7727 rs16980739 C T . PASS RS=16980739;RSPOS=16577726;dbSNPBuildID=123;SSR=0;SAO=0;VP=0x050000000005150537000100;WGT=1;VC=SNV;ASP;VLD;G5;HD;GNO;KGPhase1;KGPhase3;CAF=0.8508,0.1492;COMMON=1 +chr22 7742 rs576849325 C T . PASS RS=576849325;RSPOS=16577741;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 7751 rs140385 CT C . PASS RS=140385;RSPOS=16577754;dbSNPBuildID=78;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 7848 rs777938914 GTT G . PASS RS=777938914;RSPOS=16577848;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 7858 rs35083394 T C . PASS RS=35083394;RSPOS=16577857;dbSNPBuildID=126;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 7868 rs539417228 G T . PASS RS=539417228;RSPOS=16577867;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 7917 rs184534184 G A . PASS RS=184534184;RSPOS=16577916;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005000034000100;WGT=1;VC=SNV;ASP;KGPhase1;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 7995 rs544969179 C T . PASS RS=544969179;RSPOS=16577994;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9986,0.001398;COMMON=1 +chr22 8071 rs750059394 C T . PASS RS=750059394;RSPOS=16578070;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 8083 rs146761760 T A . PASS RS=146761760;RSPOS=16578082;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 8083 rs33970448 T TA . PASS RS=33970448;RSPOS=16578082;dbSNPBuildID=126;SSR=0;SAO=0;VP=0x05000000000517003e000200;WGT=1;VC=DIV;ASP;VLD;G5A;G5;KGPhase1;KGPhase3;CAF=0.5663,0.4337;COMMON=1 +chr22 8083 rs397709709 T TA . PASS RS=397709709;RSPOS=16578091;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050100000005000102000200;WGT=1;VC=DIV;SLO;ASP;GNO;CAF=0.5663,0.4337;COMMON=1 +chr22 8098 rs752022968 ATTACTTTGAC AAATTACTTT . PASS RS=752022968;RSPOS=16578098;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 8102 rs150281168 C A . PASS RS=150281168;RSPOS=16578101;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9974,0.002596;COMMON=1 +chr22 8148 rs531999750 A C . PASS RS=531999750;RSPOS=16578147;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8166 rs550080379 T C . PASS RS=550080379;RSPOS=16578165;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040024000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 8235 rs561895809 A G . PASS RS=561895809;RSPOS=16578234;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000100;WGT=1;VC=SNV;ASP;VLD;KGPhase3;CAF=0.9986,0.001398;COMMON=1 +chr22 8279 rs796310705 C A . PASS RS=796310705;RSPOS=16578278;dbSNPBuildID=146;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 8280 rs62228721 C T . PASS RS=62228721;RSPOS=16578279;dbSNPBuildID=129;SSR=0;SAO=0;VP=0x050000000005000102000100;WGT=1;VC=SNV;ASP;GNO +chr22 8287 rs768041822 G T . PASS RS=768041822;RSPOS=16578286;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 8300 rs576490586 C T . PASS RS=576490586;RSPOS=16578299;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 8309 rs529453609 A G . PASS RS=529453609;RSPOS=16578308;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8360 rs553157809 TAAAG T . PASS RS=553157809;RSPOS=16578360;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005040026000200;WGT=1;VC=DIV;ASP;VLD;KGPhase3;CAF=0.9986,0.001398;COMMON=0 +chr22 8360 rs367989934 TAAAG T . PASS RS=367989934;RSPOS=16578362;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP;CAF=0.9986,0.001398;COMMON=0 +chr22 8377 rs190123248 G A . PASS RS=190123248;RSPOS=16578376;dbSNPBuildID=135;SSR=0;SAO=0;VP=0x050000000005040034000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.9996,0.0003994;COMMON=0 +chr22 8394 rs566160399 T C . PASS RS=566160399;RSPOS=16578393;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8404 rs539576721 C A . PASS RS=539576721;RSPOS=16578403;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8420 rs138889000 T C . PASS RS=138889000;RSPOS=16578419;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000000005040036000100;WGT=1;VC=SNV;ASP;VLD;KGPhase1;KGPhase3;CAF=0.993,0.006989;COMMON=1 +chr22 8462 rs542308308 A T . PASS RS=542308308;RSPOS=16578461;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 8521 rs569973750 C A . PASS RS=569973750;RSPOS=16578520;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8549 rs537305556 C A . PASS RS=537305556;RSPOS=16578548;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8574 rs35576987 A AG . PASS RS=35576987;RSPOS=16578575;dbSNPBuildID=126;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 8610 rs768868814 AAAT A . PASS RS=768868814;RSPOS=16578610;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000200;WGT=1;VC=DIV;ASP +chr22 8643 rs555710025 T C . PASS RS=555710025;RSPOS=16578642;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8660 rs574024889 A G . PASS RS=574024889;RSPOS=16578659;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8671 rs1987449 C T . PASS RS=1987449;RSPOS=16578670;dbSNPBuildID=92;SSR=0;SAO=0;VP=0x050100000005150136000100;WGT=1;VC=SNV;SLO;ASP;VLD;G5;GNO;KGPhase1;KGPhase3;CAF=0.08966,0.9103;COMMON=1 +chr22 8681 rs553234471 A T . PASS RS=553234471;RSPOS=16578680;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8697 rs577654000 C T . PASS RS=577654000;RSPOS=16578696;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8700 rs760832417 G T . PASS RS=760832417;RSPOS=16578699;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 8743 rs544795206 T C . PASS RS=544795206;RSPOS=16578742;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8753 rs764274399 C A . PASS RS=764274399;RSPOS=16578752;dbSNPBuildID=144;SSR=0;SAO=0;VP=0x050000000005000002000100;WGT=1;VC=SNV;ASP +chr22 8792 rs138428270 G GA . PASS RS=138428270;RSPOS=16578791;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x05000000000517002e000200;WGT=1;VC=DIV;ASP;VLD;G5A;G5;KGPhase3;CAF=0.8606,0.1394;COMMON=1 +chr22 8801 rs563263722 C G . PASS RS=563263722;RSPOS=16578800;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998,0.0001997;COMMON=0 +chr22 8848 rs575131982 G A . PASS RS=575131982;RSPOS=16578847;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000000005000024000100;WGT=1;VC=SNV;ASP;KGPhase3;CAF=0.9998 diff --git a/workflows/variant-calling/rna-variant-discovery/test-data/genome.fasta b/workflows/variant-calling/rna-variant-discovery/test-data/genome.fasta new file mode 100644 index 0000000000..b0ea69be02 --- /dev/null +++ b/workflows/variant-calling/rna-variant-discovery/test-data/genome.fasta @@ -0,0 +1,668 @@ +>chr22 +ACTCAAGATAATGATGAGTAAAGAATATATTTCTAACAACAAAAAGGAAATTTGATAGTA +TTTCTAAAGACAAAAAGGAAATTTGTATTCACATTCAGTTAGTCATTCCACCAGAATGAC +TTCATCACACAATATTTTGTGACAAGAACCTGAACAGCCTCATGTTTTACAATATTCTTT +TCATCTTTTATTATATGCACCAAAATTTTCTTTTTTAAATTTTCTTGAACCTCTAAATCT +ACTTTAAAAATTTACCTGATACACTTTTTAAATGGACAAATGCTGAAGGTAGCTGTGTAT +ACAAATGTGACTAGAAGGAAAAAGATGATGTAGAAATACAATAACTCCTTGAGTTGATCA +TTCTGATTGGCATTTATAGAGTAGAAATGTTTTGTAATTACAGAGGAAAAAAGATGGCCT +TTCCTTCAACAGTTATGAGCCGTCAGAATTTTCAAAAATATTGCATTTTGACAATGTAGT +TTCTAGTTTGACAATGATATATTTATCTTCAAAACCAGGAAAATGTAGATAAGGATTTGG +TTTTATAATATTTAAATTCTTATTAAAATGTATAATAAAATTGTTTTCCCCATCACTTTA +TTCTTCTGTAAGTTATTTTACGTTTAAAATGTAAACAAATAAAAATAAGTAAATAAACAG +TAGCAGCTTCTTTTCCTGGTGAATCGAGGATTGAGTATGTATTATATCTTTCCTGGACTA +TTGGAATAACCTCTCCCTCCTTCCACAGAGAAGCCATAATAATCTTTATGAAATACAAAT +CAAATCATGGTATTCATTCTTTAAATAGTTATCAATAAAAATAAAATCCCAACTTTATAC +CCTGTTCTGCAAATTTTAACGTGGTCTGAATTCAGCTTACATTTCTTCTTTCCCTTGTCT +ATTGCCCATCAGGCTCACTGGCCTTATTCCTTCACACCAAACTAGTTATTTCCGGGGTGG +GAGGAAGGCTTGCAGTGTTTTCTCCATCTGCAATAGTCTTTCCCAAATCTTAGTGTGGAT +AAAGTTTCCTTCTTGTTACTTGAATCACAAATACTATGTTCTTAGTCATTCTCTGTTACA +TCATCCAGAGTACATTATATCAATTTTCCAATATTTTTATTTATTTGATTTCCCACTATA +ACAGAGGCTCTGTTAGTGCAGGGTCTTTTACTCTTTTGTAATCCCAACAGCAAGAACAAA +ACAAGGTACATAGTACATATTTAATAAATACCTGTTGAACAAATATGTGCCAGTAATATT +TCTTCATGCTGCTGAATAAGTTAACAGCATATAAACACATACAAACCAAGTGGCATGGAT +GTCTGCTTTGATTTTTAGCCATTTAAAAATATACGTAACCCATCCTAAGGGGTTTATATT +TGTTTTGCATAATACATTAATATGTACTCATTATTCATTACACAGTTAATATATCTATAT +TTGCAGGGAATATACATTGCTTGGAATTATACAAAAAAATATTATTTTTCGTTTTCTAAT +ATTCAGGATACAGTGTTTTAATGGGGGTGTTTCTTCATTCTTTTTTTCTTACTGGTTTTT +ACTTTTTAAATTTGAAAGCCTTGCAGTGATCATAAGGATCTGTTCAGGCAAAGAACATGA +AAGAGTTTAAATTTTTATCATTTTAGTGTTTCTTATTCTCTATATCAAAAACATTCACAG +GTAAGTTAACAAGATCCTCATCAGGAGGAAAAGTAAATTGTTCACTACCATCCTCTAGTA +TCCTAATCTGGTCTTGTTGTTGGCTAACTTCAGCAGTTACTATTCTGTGATTGGTGTAAT +ATTAACCAAATAAATTACTGGATTTGTTCCACAAATATTATATCTTAGATTGGTTCTTTC +CTGTCTCTGAAAATAAAGTCTTGCAATGAGAATAAATTATTTTACAACAGTTAATTAGCA +ATGTAAAGTTTATTGAAAATGTATTTGCTTTTTTTGTAAATCATCTGTGAATCCAGAGGG +GAAAAATATGACAAAGAAAGCTATATAAGATATTATTTTATTTTACAGAGTAACAGACTA +GCTAGAGACAATGAATTAAGGGAAAATGACAAAGAACAGCTCAAAGCAATTTCTACACGA +GATCCTCTCTCTGAAATCACTGCGCAGGAGAAAGATTTTCTATGGACCACAGGTAAGTGC +TAAAATGGAGATTCTCTGTTTCTTTTTCTTTATTACAGAAAAAATAACTGACTTTGGCTG +ATCTCAGCATGTTTTTACCATACCTATTAGAATAAATGAAGCAGAATTTACATGATTTTT +AAACTATAAACATTGCCTTTTTAAAAACAATGGCTGTAAATTGATATTTGTAGAAAATCA +TACTACATTTGTAGTTGGCACATTAAATGCTTTTTCTTACTCTGAATTCCTGATATGACT +TTCTTTAGGATTGTTTAAAATATTCTAGTAGTTTTAGGTCAATTTAGATGTGATTTAGTT +GCTCTAGATATTATAATTTTTAGGGGTTCCCTTTCATTTTTTTCTTACGTTTCTTCAAAT +AGTATAATGCCTTATTTTCATTTATGAAGAAATTACCCTGCTGTTGGTGATACGGGTATA +TTTAAATAAACCAGTTGCAGTGCATTTTTGCAGAAAGTCCATTAAGACATAAATTTTGTC +CAGTAACCACAGTAGAAGTGGTGACTCTATGATTCATTCATGTTGCATAAGTAGGTGAAA +AATATGAGCTATATTCTGTCTGTTAAATGGAATTCTAGAGATGAAGTAGCCCAGGTAAAT +GTATGTTTGAGATTACTAGATAACTGTTGTACAAATTGGTATGTCACTTAAATTGTTTTC +TCTCAGAAAGTCCACATAAATAAATGAAATAGACTAATAATAGTAATATGGTGTAGAAAA +AACTCCCTTAACATTATTTCCATAGATAAAACTAATTAGAACTGTAAATTCTAAGGAGAT +TATTTATCTAAACTAATTTTAAAATCAGAAGTTAAGGCAGTGTTTTAGATGGCTCATTCA +CAACTATCTTTCCCCTTTAAATATGATTTATTGTCTTTCTCATACACAGATGTATTGCTT +GGTAAAAGATTGGCCTCCAATCAAACCTGAACAGGCTATGGAACTTCTGGACTGTAATTA +CCCAGATCCTATGGTTCGAAGTTTTGCTGTTCAGTGCTTGGAAAAATATTTAACAGATAA +CAAACTTTCTCAGTATTTAATTCAGCTAGTACAGGTAAAATAATGTAAAATAGTGAATAA +TGTTTAATTACAATAATAATTTATTTTAGATCCATACAACTTCCTTTTAAAAAACCTACT +GCACTAACTAGTTTTATGCTTAAAAAAAATTATTACCAGTAATATCCACTTTCTTTCTGA +AAAAATTTTCTTTAGATCGGCCATGCAGAAACTGAACCTGATTTGTTTTTTTTGAATCAC +CTAGGTCCTAAAATATGAACAATATTTGGATAACTTGCTTGTGAGATTTTTACTGAAGAA +AGCATTGACTAATCAAAGGATTGGGCACTTTTTCTTTTGGCATTTAAAGTAAGTCTAATT +ATTTTCCCATTAAATTCTTAAGGTACATATTACTTGCTTTCTTAATAGATTTATAAATAT +GTATTACTTATATACTTTTGTTTATGTTTGGCTGGAAGAGTTTTCCATACTAAAACTATT +TTGTACCAGTGATGAGCTTCTCAACTTTTGCTCTTTGAAATTTAAAAAGTAATAAATTCA +AAACTAAATTTCAGTCATGAATGAGAGCTTAAATATTTTTAAAGATTTTTGTTCTACTTA +AGTAAAATTTTCTAGGTCCAGATGAATATTGCTGTAGGTTTCACTGTGTGTATGGATTAA +AATATCCCCAAAAAAAGAAAAAAAATGTTTTACCTTGAGATTCAGAACAATAATGTCAAA +CTCCCGTGGTTCTTACTGAAAAACAAGCTAATTAAGAATAAAAAATGTTTTGTAGAATGT +GATATATGCAGTACTCAAAAGTTACAGGTCATAAACCATATAACTTTTCATAAATTTAGA +AACAGATTTATATCTAATATGATATTTTAAGTGTTAAAATTTAAAAATGGAACCCAGAAG +TTAAGTTGAAAACAAGAAGCGTAGACGTGTGTCAGAAGAGTCAAACAGCATTCACTGAGC +GCTTTGTTCCCTCCCTCTTCATTTGATTATTTTTGTGCTCAATTTCCTTTTTTCATGCTT +TTATATCTTGTACTGAGATTAGTCAATGAAAACTAGTTGAAATAAACCTAAAAACTAGAT +GTTTATTTAATCACATATTCAGGAACTACCTGAAACTCATGGTGGTTTTGCTTCTAAATT +ACAGGTTTTGAATAATGTTATTATTAGTATGATTGTAACATTTATTGGATTTCAAAAATG +AGTGTTTAAATTGTTTAGCAAAGATTATTTGTATACTGATTTAAGACTATATATATATTT +TTCTAATTTTGCATGATTCTTTTAGATCTGAGATGCACAATAAAACACTTAGCCAGAGGT +TTGGCCTGCTTTTGGAGTCCTATTGTCGTGCATGTGGGATGTATTTGAAGCACCTGAATA +GGCAAGTCGAGGCAATGGAAAAGCTCATTAACTTAACTGACATTGTCAAACAGGAGAAGA +AGGATGAAACACAAAAGTTGTGTGACTCTAGTCTGTGTTTGAGACTCTTTTCACTGCAGT +GGGGCAGAGTTGTTTAGAAGCCCAGTGTATATACAGATCATGGTCCTTGGAATCAAGCAG +ATTAGGATTTGGAACCAAGTTCCACTGCCTCTCATCTGTGTAGTGTTAGACACGTTATGC +AGGCTCTCAAGACTCATTTTCTTTGTCTGTAAAATGGGAATAATACCTGCTTCGTAAGGC +CATTGTGAGAATTAAATTACATGAGATATGCAAAGAACCTATCACAATCCTTGGAACACA +GAAGGTGCCCAATAAATGTTAGATCCCTTTACTTTCCCTTCCTTTCTCTTATTCAGGTCC +CTAAGTATTTACAGTGATTATTTCCTTATTCTGTCATTTATTATCTCTCAGTAATGACCC +TGAAAATGAGTGGAAAGAAGTTAGTTTTTACATTTCCAAGTTTAAAATGGATTTCGAGTC +ACTCAGTAAATATATCACACCCTCTAGTCATCTGCTGTCTAGCTTAGTGTAACTAAGAGT +AGGAAATACAATGTAAACTTTTTTTTTTGAGACAGGGTCTGGCTCTTTTGCCCGGCCTGG +AATGCAGTGGTGCAATTTCGGCTCACTGCAGCCTTGACCTCCTGGGTTCAAGCCATCCTC +CCACCTCAGCCTCCTGAGTAGCTAGGACTATAGGAGCATGCCACCACTCCCAGCTAATTT +TTGTATTTTTAGTAGAGACAGTGTTCTATTCTGCTTTATATTAAAAGCCCCTTAGAAAAT +GGGAACCTGGTGAATATATAATGAATTGTAAAATATTTTAATGTGTAACTTTTTCAACTG +TGAAACTGACTACTGATTTTTTGATGAAAACAGCTGCTGATAAAGTATTTTGTGTAAAGT +GTAGTTCTTATTAATCAGGAAAATGATGACTTGATTAGACTGTATATGCCCTCTTGGATT +TTATTTTAAATGGATTGGTGACTTTCACATAGGTAAAACACAGTCCATCTGTATTCTTTT +TTCCATCAAAAAGCGAGTGATTTAGAATTATAAAAAAATTTGTGAGCAGCCTATTTGAAA +GGCATCATGGAAATTTCACAGCACAATAACATGGATTTGTTTTTTTCTTAATGATGTAAA +TCCGTTTAATTCATATTTTGATCAATAGCCCATGCTTGCCAACTCTGAAGAAATTTAATT +TCCAGCAGTATTTTAAAGCTAGCCTGTTAACTTTTTCTGAATATTTAAAGTTCCTCTTTT +TTCTATGTCTGCACAAACTGCAGACCTGGGCTGGACCCACATACTCAAGAGTCCACCTTA +AGAAATTATTTTGATGTCCAAGACATCACTAAAATATTTCAGTTTAAAGATAACATGTGG +TGTTAATAGATTGTGGTGCTTTTACTATTTAAAGACAACTTTCATACTTCAGATGTTTTT +GAGAAGAGGGGAATGTGAGGGGAGGGGGCAGAACAGGGAGGAGTTTGAATGAATTACATT +CTTTATATCCATCCTGCTCATTTGGGGCATGTCTTTAAGAGAAGGCTGAAAGTTGTGAGA +GTATATTGTATACCGTAAGAGAATCAACTCTTCATCATGGATGGGATTGTGAAGGCTGAA +CTGTAAAAGTCAGCATTGACAGCATCCTCAATTAATAATTCTTGGTGACAGAATAATACA +GCTGGGCTGTTTTATAAATATAAACAATACCATTTTTAATTATTACATTAAAAATTTTAA +ATATATCTATGTGCCATGGCCTGGGAAGCCTGTTTTCTATTTTCATAAAAATTATTTTTA +CTGTATGAAAAGATTATGGGGTTTAGCTCAAAATATCTGTGGTCCTGATAAAATTGGATT +GGTAACTCTACCTCAGAAGGAAAATGGGAAAAAAAAATAGATGAGTCACAATTCAATACT +TCAAGCTCAGAAACTGTGCAGATCACTGAATTTTAGATTTATAAAGTCAGAGTTGGCATG +CGTTGTTTTTAATGATATGGAAGACCTTAAGAAAAAAACTTGGCTGAAGTTTAATCGTTG +GTCCAGCCATTTGAAAAAGGCAATAGTTCGAGGAGGTTTCCGAATTCGGCATTTGAAATT +CATTTTGTTCTCTCTTCTTCATTATTAGTGCATTTGGTGTGTGTATACTTGCACACAATT +CTGTTTGTGTACACACTGCTTGCTAAGCCCTAGTCAAGAGGCATCTTTTATAAAAGGTGT +AAAGAAATATCAAGGTTCTAAAATTCGGAAGAGTTTAGAATTTATTAGGAGTTTCCCAAG +TTGGGATGTTAGTCTTTAAATAAACTTCATGCACCTATTCCACTTAAGGTTTTGCACCTC +CTTTTTATTAGTGCAGTGCCATTTCTTCTGCTTGATTTTAGGTATGTTAATATTCCAGCC +TTGCTAGTTAGCATAAAGTGACAGGTGTGAGCCATGAGGAAATTTTCTGACTTAATTTTT +ATACAACTACATATGAGTTTTAGTGGAGAAAAAAAATTAGTCCCTTGTGCATATATAGTA +GTTAGGTAAATGATTTTTCTACCAACAGTGTACTCCATTCCTCATGTAGGTAAGTACAGA +AAAGGTTTTTAAATGTATTTTGTTAGCCAGTTAAAGTCTATGAATCTATCTGCAACCTTA +TTTAATCTGTCACTACAATAATTTTGTGGTTATGCTAAGAACCATGTATACTTTTAGGTA +TTCTTATTTTTGTCAATTTTTCTAGGTTAGCAAGGAGGCAGAAAAGCTTCACTGTTTCAT +ATTAAAATATAATTAGACTAAACTTAATTCTAGTATGAATTTCCAAAATCATTATCTATT +TATTTCATTTTTATTTAATTTTGTTTTTAGTTCATTTTTAAAAGTCCCTTGTTCAATTTA +ATTTATGTTCCTAAGAGTGGTTGGAGAACTTGGCCTTCATCTGATTTCAAAAACATTTTG +AGTTTCAAATGAAGTTAATGGTTTCAGTGTGATTCAGTCCTCAGACCTAATTGGGTTGAA +TAAAATCTAAAAGAATATACCCTTTTGGAGCATAACATTTTAATACCTTGAGGAATGTGG +CACTACCAAAAGAAGACTACTAACACGTCAGATGTTCACCTGGAAGCTTTAACAAGAAAT +TCGAACCACCCTTTTGGCCCCATTAATTGTAGCAAGTTTATTTCTCTATATTTTGTCATT +CAGTGAATTGAAGTCCTGTGGTATACTGCATTCATTAGAAGAAAAACGTTTTTAATGTCC +TTTTAATGATGGCCCAGAAAGCATTTGACACAGCAAGATGCATGTATTATTATATTGAGA +ATACAGAATAATAACAGTATCACTAAATTTAAGACCTCTTCCCAGTCTTGCTGTTCCTAG +CAAGAAGTTTGGCCCGTGACTGCACTTACTGTTTATGCTCATCAGAAACTGTCAATGTCT +GCTTTTCTTTAACTCTGCAGTCTGTAACATCATGCTGTTTATTAAAAAAAAAGAAAAATT +ACTTTGACTTGTGTCCAAACAATCCTTAGTGTACTACATAAGCAAAAAACTGTGATAATT +CTCTTTTGCCATTCCTTTTGAAAAGCAAGCCAGTGTTGCTAAAATCAAAATTTAGCTGAA +TTTGAGTTCTTTTCAGTAATGACTAAGAATACTTGATTGAAAATCTGAAACTATTATACC +TTAAAAGCCAATTTTTCTGCCCCAGTAAAGTGATGAATATTAAAGAAATGTATGTTTAAA +TATTTACTTCCTTTAAGCATAAAGAATTATATGCTTGTATTTTAAGAAATATATGTATGT +ATACATACATATGAATGTATGTATATGCAATAGGTAAGTGGACTTTTTTCCAAGTCATTT +GAAGATCAGAACCTAGAAATGAAGTTAGGCTACAAGCAAACTGGTTTTGCTTTCAGTTCT +CATAAACATTGCAAAAGGTAAGTGTGGGCTTTTCTTTGACCATTAATGCACATAGGCATT +AACAACTTAGTATTTCTGAGCAATTAAGCAAATAATTACTTACATTTTATTTATTTGCCA +AATGGTTTAAATAATTTTGAATTGACTTTGCTCTCCAGGGATAATATCTCTCTTTGCTGG +AATGATTCAGGTAGCTCCTATCTAAATGGAAAACTGTGGTAATTGAAACACACACTTTAC +ATTTTAAATTAGCAGTTTTGAATTTGTTAGGGAAAAAAATCCCAGCAATTGCATATTGTT +AGGTAGAAGTCAAATTTACAAAGAAACGGAATAGAGATGTGCCCTTGAGAAAAGTGTAGA +ATCTCAATGTGCAGATGATTTAAAATGTGCGTGCATATAAAATGTTCATGTGTACTTACA +TACTTTATTACAGAGAAGTCTTTGGTATACAAAATAGTTTACCACAACCTTTTAAACAGC +AGGTTCTGGGCCTTAAATGCGTATCACATTTAGCCAAGAGAACTCGGGTAGGGGCATGGA +AAATGAACTGCAGCTCCCTATCCCTAGCCTCTATACCAGCTGTTCAATGAAAAGTACCAA +GGCTCACTGAATGTTATAACCTAGCAGATTGTTACATAAATGATCTAACATTTTTGAGCA +CCGCTACTGGATGCTAGAAGCTAAGCTAAAGTGTTTCACATGCCCTACTTTGCTTATTCT +ATAAAATAACTGCGTGAAAGAACAGGTTATCCCCATTTTATAGATGAGAAAAGAAAGGTT +TACACAGGTTAGCTTATTTGCCCAAAGTTGTGATTATGGCCTACAAAGTCAAATAAATCC +TACTCTGAGACACATGTTCTTTCCACCATTGCACACTAGAAAGGAAAACACCAAGATTAT +TCATTACTGATCAAGTCAATATTGCTGTATTCAGCTAATTTAGTAATATGTGTCTTGAAA +TTAATTGCTAAAAGGGATTAAACTGACTTAGAATCAGTTTTTTGTTTGATTACATCTACA +TACAAAAGTAGCTTCAAATGTCTCATTCTACTGTCCATAATTTAAGATTTTTGAGTATAA +TACAATTTTAAAGATACTTTGAGGCACTTTGGAAAATCAGACCAAAATCTCTTTTCCACT +CACAGATTCGGCTTAATCAATCTGGAAAGCATTTGTTGAGAGCCTTATGACATCATTTAA +TAACCACGGTTGATTCATTAATTAAAGTACAGACAATTGTTGACTATCCATGTGGGACTT +TTCTATTAGGTTGACGCAAAAATAATTGCGGTTTTTCGCCATTAAAGGTTAACAGCGAAA +ACTGGAATTACTTTTGCACCAGCCTAATACGATGTGGATCATCTGAGATGAATGTTGAAA +TCCAGTATAGCTTCTTCATATTTCTGGCCCATTTTTCCCACCAGAAAGTGCACAAAGTGA +AATGAGCTTATGAAAAGCTTAATTAACTAGAAAAATGTTACTGAAAGAAAAATTACATGG +TACATGACAAGGCTAAATACTAGTAACTCTAAACTTAGTGAATTTTCTAGGCAGCAGCTT +TCCTCTGCTGTCTAGACTGGTAAAGAACAAACTAAGGCCAGGCGCAGTGGCTCATGCCTG +TAATCCCAGCACTTTGGGAGGCTGAGGCGGCCAAATCACCTGAGGTCAGGAGTTCAAGAC +CAGCCTGATCAACATGGTGAAACCCTGTCTACACTAAAAATATAAAAATTAGCTGGGCGT +GGTGGTGCACACCTGTAATCCCAGCTACTTAGGAAGCTGAAGCAGGAGAATTGCTTGAAC +CCAGGAGGCAGAGGTTGCAGTGAGCCAAGATCACGCCACTGTGCTCCAGCCTGGGCTACA +AGAGCAAAACTCCATCTCAAAAAGGAAAAAAAAGAAAAAAACTATAATAAATATGTTAGG +TCCATGTTTTCTTAAGTTTTCTACCGGATTTTTATCTTCGTATAGTGAACGAACTGTTAA +GAACTTTTTTATGAGAAATATTTTAGTATGACTATATTGCATAGAGTTAGGCTGATGGTT +CAGTGTTCAGTAGGTTAGATACCCTCATTGTTTATTTCCATATTGACTGGTTCTAGCTAG +AGCTGAAATTAGGCAAAGAATATCTTGAACTCATTTTGCTATACAGGAAAAAAGTGCTTC +CTTAGCTCATTTGGAAAGAGATTGAGATTAGAAAAGATGGTTAATTTGTATGTATTTATA +GAAATAAATAGAATACAAAATGAGGCTTTTAAATTTTTTCCCACATGAAAATATGATACT +TTAATCATTACGTTTTACATTGTTAGTTTGCAGACAGGCATAATTAGGTCCTCAGTTGCA +GAAATCACAGACATCTGAAGGCCAGCCCTTTAATTTGGCCACCGTCTTAAGATTTCTCTG +CTCCTTCCTTTGCTCCTCCTCCTACTGCACAGTTTGAACTGATGCTGTTCTATATAAGGT +ACTTTTCCACCTACCTCATCTCTGACTACAGTGCTATATTTTTCACACAGTAAGGACAGG +TGTTGTGTTAATCTCACCATGCCAACAATCAGGGCACCACCTAGCAGAGTCAGTGAAGGC +CAAAATAAACAGTGGAAGATAGCCATTTGGTCATACTTTTTTATAAGAATGACATCTTCA +GATTGGCTGGCTGGACTGTAGAAGCATGAAAAGGGGGTTCCATTTTTGTGATCGAAGAAT +TCTTTTATGTCCAGAGCACTGTTGAGCAAATCATTTCTATCTTGGTGGCACTTAGGTGTG +TAAAAGCACTAGGAATATGGAAGAGGGAAAAAGATAAAGGCACTGTCACCAATACCAAAT +ACTTAACAGTTTCTAATTATGAAATAGCTTCAGGCTGAAGTTATTAGTGGGCAGTTTCAA +TCTTAGAAGGTGGTAAAATATTACATAGCTCATGGGAAAGGGTTGATTGGAGGGCCACAG +TGAAATGGCCATTTCCAGTCATTAAGCAAGGATGTGGAAGAGAATTCTTAGTTTATATGA +CATTGCAGGAGAGTCAGTGACCAATTTCATAAGGAATATGACTCCTCCCTACATGCAGGT +TCTTGGACTCTTGGACAGTATGAATCCGTTTGTCCATTGAACAAAAATGTATTGAGCCTT +ACTATGAGCTTTCAACACCTAGTAATGCCTCTGTGGTCTCTGTCTTGATCTCCTGTAGCA +AAATATTACCCTGAAGAAAAGCACGTTGAGGCTTTTGCTCTAGACTCACAGACAGGGAGC +CCCACCTGGACTTTGGTTCCTGGGAGACAGAACCAGTGGAGAAGGGAGCTCTGTCAGCTG +GTGACTTTTTTCAAAAAAGCTTGAGGTTTATTACCATATCCATTAGGTACTTGAGGTACT +GTGCTAAAGGCCTACAAACTGTTTGAAATCTTAAAAATCATTGCATCCAAAATAGAAAAC +AAAAGTCATCAGATTGAAATTGATGCTTAAAGACAATAAAGTGTAACATGTCAACTAATC +TAACACAACTCAACTTTTATAGTTAGGTATAAATATAAATTTTAAATCATATGAAAGACT +ATACTTTCAGGGATCATTTCTATAATTCGTTAAATCATATGAACCCATTGTGTAACTTAT +TAAAATAAAAATAATCTTTACATTTATTTGATAAGAAAAAATTACTCGCTTGATTCAAGG +GAGACTGTGGTACACTGTAGCATATGTTATATGGCGCGGAGTGGAATCTCCAAAAGAAAG +ACTCCCCACAAATGACTACTCATTGGCTCAGCCTATAAATTCCAGACACCAAGTTGTGAA +ATTGGAATAATTTCTCTCCTTTCTATATACCCCATTTCTCCACCAAGAAGAAAGCTTCAT +TTATCCTGATTTGATCACTATAAAAATGTTCACTCCAAAAAAATAGATTTATCCCTAAAG +ACAGCCCTGGGTTATTTATGTACCCTGCTAGGGACAGTCTGGCAGGGAAAGGTTGCTGTC +ATAAGAACTCTTTAAACTTTACAATACCTTGGGATTTATCTGGACAGCCTCTTCATTATA +ATGTAGGAGAGCTTTCTGAGCTGAATGGGTGAGGTTCACAAACACCCGAAGACACGAGTA +CTTCCCGTGACCACGGCAGTGCACACCACAGGTGAAGGCACAGTCCAGCCAGTCGTCCAT +GATATCTGTGTGGATGGCAGTGCAGGTTGATTCTTCTCTCCGAATGCTTCAATTTGAAAA +AAAAAAAAATGTTCTTCACTTACTAGAAAATTTCGTTCTACATTTTGGTGCGGTTATGAG +CTTATGTACACAATTAGCTGGGATTACAGGCGCTCAGCTGCCATGTCCAGCTAATTTTTG +TATTTTTAGTAGAGACAGGGTGTTGGCCAGGCTCGTCTCCAACTCCTGACCTCAAGTGAT +CCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACTGCACCTGGCCC +AAATACTATGTTTTATCAATTCTAAAGTGCACTTTAGTATTTACATTTTAATATAACTAA +AATCAATATGTATTTTGCAATCAATGGCATCTTGCTATTATTTGAAAACATTTCTTTAAT +AGTCTGTAAAATAATGGAACATGCCCAGATGCAGTGGCTTATGCCTGTAATCCCAGCACT +TTGAAGGGTCAAGATAGGAGGATCGCTTGAGCCCAGGAGCTGGAGACCAGCCTGGCCAAT +ATAGTGACAGAATAAATAAATAAGTAAATAAAATAATGGAAAATCTCACAAATGGTGATG +TTTTAGGTTCGACAAAATACATTAACTAGCCCATTTAGTTTTCTGAAATTATTTTGATGT +TATTGCTTACAATATTTGTTCTGTGGTACACAACCATAGGATTAATAATATTGATGAAAA +TAATAAAAGAATAATAAGCATGTATTGAGCTCTTCCTGTGTGAAGTTCTGGACAAATCCT +CATAAAGCCTTAAAAGGCAGATACTAGGCTGGGCACGGTGGCTCATGCCTGTAATCCCAG +CACTTTGGGAGGCCGAGGCAGGCAGATCACGCGGTCAGGAGATTGAGACCATCCTGGCTA +ACATGATGAAACACGGTCTCTACTAAAAATACAAAAAATTAGCCAGGCATGGTGGCACGT +GCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAAAATCGCTTGAACCTGGGAGGCT +GAGGTTGCAGTGAGCCAAGATCGCACCACTGCTCTCCAGCCTGGGCGACAGAGCAAGACT +CTGTCTTAAAAAAAAAAAAAAAAAAAAGAAAGAAACAGGCAGATACTAGCCCAGGCACGG +TGGCTCATGCCTGTAATCCCACACCTTCGAAGGCCCAGGCGGGTGGATTATCTGAGGTCA +GGAGTTTGAGACCAGCCTGACCAACATTGTGAAACCCTGTCTCTACTAAAAATACAAAAA +TATTAGCCAGGTGTGGTGACAGGTGCCTGTAATTCCAGCTACTCAGGAGGCTAAGGCAGG +AGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCTGAGATTGTGCCACTTTACTC +CAGCCTAGGTGACAGAGGAAGACTCTGTCTCAAAAAAAACAAACAAACAACAACAACAAC +ATCAAAAAGAAACCTATAGTAATAAAATTGAAATAGAAGGAGGTTTGCAATCAAAATGAC +TGACTAGGAATGAAATAGGAAACATAATATTTTGCATCTGCATAGGGAAGTCTGAGATTG +GCTGATCTTGTTCTCTTCTGTAGGGGAAATACTAGTCCAGAACTTGGGGTGCCTGCCAAG +AGGGGAGCAGCCACAGTAGGAAAGGGGGACTCTGGAATGCTAGGGTTCTGGGGTCTGTGG +ACACAGGAGGCAGAGGACATGTGTTAAGATGTTTTAAGAAATGAATGTTGAACTGGATAT +GAAAATATTTTTCAGCCGGGCGCAGTGGCTCACGTCTGTAATCCCAGTACTTTGGGAGGC +TGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACC +CCGTCCGTCTCTACTGAAAATACAAAAAGTTAGCCAGGCGTGGTGGCGGAGGCCTGTAAT +CCCAGTTACTCTGGCGGCTGAAGCAGGAGAATGGCGTGAACCTGGGAGACGGAGCTTGCA +GTGAGCCGAGATTGCACCAGTGCACTCTAGCCTGGGCGACAGAGGGAGACTCCATCTAAA +AAAAAAAAAAAAAGAAAGAAAATATTTTTCACTATAGAGAGGCATATGTCCCCTGAACTT +GCCGGGATCCACCTTTCCTGCTGGTGCATTCTGTGAGTTAGAAGAAAACTTCCAAAGAGC +CATTTTTTCCACCCTGTCTACTGTATAAAATTGCTTCTCAAACATGTGCTGCATTGCAGA +GGATTACCATTGTTTTGCTAACCAGCGTCTGGTCTTTCTTATGTGGCGCTGCAATTACTA +GTGTCAAACCCTGTTGGTAATACCCAGAGGACGGTGTCTGAAGTCTTTACTCAATATTCA +CATTTGGCCGGGTGTGGTGGCTCACACCTGTAATCCCAGCACTTTCGGAAGCAGAGGCAG +GCGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCATCT +CTACTAAAAATACAAAAATTAGCCGGGTATGGTGGCGGGTGCCTGTAATCTCAGCTACTA +GGGAGGCTGAGACAGGAGAATCACTTGAACCCAGGAGGTGGAGGTTACAGTGAGCCAAGA +TTGTGCCACTGTACTCCAGCCTGGGGGAAAATTCACATTTGTAGAGAGTTTAAATTCTTT +TTTGATACGGAGTCTCGCTCTGTTGCCCGGGCTGGAGTGCAGTGGCAGGGTCTTGACTCA +CTACAACCTCTGCCTCCCAGGCTCAAGGGATTCTCCTGCTTTAGCCTCCTGAGTAGTTGG +GATTACAGGCACCCACCAAAACACCTGGGCAATTTTTGTATTTTTATTAGAGACAGGGTT +TCACCATGTTGTCCAGGCTGATCTGAAACTCCTGACCTCAGGTGATCTGCCTGCCCTGGC +CTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCACGCCCGGCCGAGAGTTTAAATTCT +TAAGTCCTACACTCCAATGTGTGGGAAGTATTCGTGCTATGCTTTTATAACTAAATCATC +TCAGTATTTCTATTTCTAGCCCCCTTTTTCTGCCTGATGGTAAGATACTTAATCTAGTCA +ATTCCAGGTAAACTTTGGCCTTTTATGATTTTTCCTGATCAGGCCAAACCTCAACCAAGT +CCCTTCTTGATCTTCTCCTTCACCTCCTTCTCTCATTCACCCGACAATTAGCCTCCAGTC +CACGGGCTGATGCAGCATCTTGGTGTCCTGTGGTCTGAGGTCATTTTCTGTCTTTCTCAA +GCCTCAGCTAAAGTTTACAATCCTACCTTTTCTCATGACCTTGAAATGCCCTAAGGTTCA +GGGGCTTCATGGTTGCTGCTTCATGGGGGAACCTGGCTGTTCTCTGAGGCTGCTCGGCCG +CGAACACCCCATCAACTACCCGGGGCCCATCTACGCCCGAGGCCTCAGCCATTCCTGCTC +TACAGCTCTGCTGTCCCATTGGCACAGGGAACTTCTTGGGGCCCCAGGGTTCCAGATTGG +AAGCAGAGAATCTCCTCTGTTCTCAGACCCCCAAACTTTGTTGTGGATTCTAATTGTCCT +TTCCCCCATCTCACTCCTTGGAACCCACTGGGAGGTGAGTAGAATCCCTGTCAGAGATTC +TACCACCATCTCCCTCATTCTTACCCTAACTTTCTTCCTCTTCCTCCCTAGTTAGGAAAG +AGGATCTTTAGCCTGCGGCGGGGGGGTGGGGGTGGGGATGCTTGATGTTTCAGGGGAAAA +GGTGACTCAGCTACTTTTGGAATATCTGTCATACCTGTCTACTGGTGCAATGAGCTGGGA +TCACACCACTACACTCCAGCCTGGGTGACAGAGCAAGATTCCATCTCAAAAATAAATAAA +TAAATAAATAAAGACTCTGGAGAAACAACTCAATACACATGAGAAGAGGCTGGCCCATGT +AGGGAAAGGACTGGCAAACTATGACAACTCTTTTCTGTTGTTTTGTTTTCAATAGTCTCT +TCACAGTTCTTTTCACAGTTTGGAATTGATACCTTTTTCTCTTCATCAGAACTCCAATGT +TTTTGTAGATTGAAGTCTTTTTTTTTTTTTTTCTTGAGAAAGGGTCTCACTTTGTCACCC +AGGCTGGAGTGCAGTGGACCAATCACTGCTCACTGCAGCCTCGACTTCCTGGGCTCAAGA +AATCCTTCCACCTCAGCCCCCCAGTAGCTAGGACTACAGGTGTTCACCACCATGCCCAGT +TAATTTTTATTTTTTAATGTATTATTATTATTATTATTATTATTATTATTATTATTATTA +TTATTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGCGGCACCATCTCGG +CTCACTGCAACCTCTGCCTCCTGGGTTCAAGAGATTCTCTTGCCTCAGCCTTCCAAGTAA +GTGGGACTACAGGTGCATGCCCCCACACCTGGGTAATTTATTTTTTTGTAGAAAAGGGGT +ATCAGTGTGCTGTCCAGGCTGGTCTCAAACTCCTAACCTCGAGTGATCTGCCTGCCTTGG +CCTTCCAAACTACTGGGATTAGAGGTAATGAGTCACCATGACTGGCCTACGTATAGCCCA +AATGGATGAGCAGTTCCCAAGGCTCATTCCCAGCCTCCACTATCCAAGTCAGCCTCTCAT +CTCCTTCATTTCCCAGGACTTAGTTCTCATTTTCCTCCCCTGTTTTCTCCGGATTGTGGC +TATTGTTCCCTGGTTGCTAGATCAACCTGGAGCACAGTAAAGCAGTGTCACAAAGCTGGA +AGGGGTCTGGGATGAGTCCACCAGCTACAAGTTCTTATAGAAAACGTACTCCGGGGATGG +CCGGGCCCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATC +CCCTGAGGTTGGGAGTTCGAGACCAGCCTGACCAACATGGAGAAACCCCGTCTCTACTAA +AAATACAAAATTAGCTGGGTGTGGTGGCACATGCCTGTAATCCCAGCTACTAGGGAGGCT +GAGGCAGGGGAATCGCTTGAACCTGGGAGGCGGAGGTTGCGGTGAGCCAAGATTATGCCA +TTGCACTCCAGCCTGGGCAACAAGAGTGAAACTCCATCTCAAAAAAAAAAAAAAAAAAGA +AAATGTACTCCAGGAATTGTCATTTCTGAAATTCAACAGCTTCTGGAATTGAAGCAAACA +GCTCATCTTGGAAGAGAAATATGTAGCCAACTCCAAAGCCAAAGCCTTTGAGTATTGAGA +CCTAGCATGCTAGGAGACCTTGATCCTGTAACCTCAGAAGAAGAATCTGGATCTGGCCAA +ATTGAGGTCAAATTCTGCTCAACTTCTCCATAGTCAGTAGGAGAAAAAAACCAACTTGAT +GTTTGAGTCATATGTTTTGACAACTAAAGAGGACACTTATGCTGGGGTCGGTGGTTCATG +CCTGTAATCCCAGCACTTTGGGAGGTCGAGGCGGGTGAATCATTTGAGGTCAGGGGTTCG +AGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACAAAAAATTCAAAAAAATTGGCT +GGGGGCAGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGATGGGTGGATCAC +GAGGTCAGGAGTTCAAGACCAGCCTGGCCATTATGGTGAGACCCTGTCTCTACTAAAAAT +ACAAAAATGATCCGGGCATGGTGGCGCACGCCTGTGGTCCCAGCTACTCAGGAGGCTGAG +ACAGAAGAATCTCTTGAACCTGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACGCCACTG +CACTCCAGGCTGGGTGACAGAGTGAGATGTCATCTCAAAAAATAAATAAATAAATAAATA +AAATTAGTCTGACTTAGTGGCGGGCCCCTGTAATCCCAGCTACTGGGAGGCTGAGGCAGG +AGAATCACTTGAACCCGGGAGGTGGATGCAGTGAGCCAAGATCATGCCACTGCACTCTAG +CCTGGGCGAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAGACACTTAAAGATG +ACATTAAAGAGGATACTTAGATTCTAGACAAAATCAAGATATAGCAAATTGGGGTGGGAC +ACACCTGTAATCTCAGCATTTGGGGAGGCCGAGGCAGGTGGATCACCTGAGGTCCAAAGT +TTGAGACCACCCTGACCAACATGGCGAAACCCCGTCTCTACTAAAAATACAAAAATTAGC +CAGGCATGGTGGTGGACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCA +TTTGAGCCCAGGAGGCAGAGGTTGCAGTGAGCTGAGACTGCACTGCTGCACTGGTGCCTG +GGCCACACCAGTCACTATGCCTGGGTGACAGAGCAAGACTCTGTCTCAAAATAAATAAAT +AAATAAATAAAATTTTGTTTTGCTGTGTTGCGGCTAATATGCGTGCTATAAGACAATGGT +TTCTTGAGTCTCATTCTCTCTGCATATGCCTAAAGCTTTTTTATTTTTATGATTCTAAAA +GATTGTACCTTCTCATCTCCTAGATTCTGTCCCATAGGTTCTGATTTTTCCTAGAGTAAC +TTGGAAGTTAAAAAAGTGGAAAAAGCTTTGCGTATTAGGTGCCAAACCCACTCAGCTCTG +CTCAAACCCCTTCTTTAATGCCCAAGGTTGTCCAATCCTAGCCCTTCCCCCTACCCTCAG +CTTTCTCCTCACCTACACAGCAACCTTAGTATAGTCCTAAAGTATGTGTTCTTATCTTCT +GTTATCTATGCCAAGGATGTTTGCTGGTTTTGTTTTGTTTTGTTGAGACAGGGTCTTGCT +CTGTCTCTTAGGCTGGAGTGCAGTGGCACAATCACAGCTCACTGCAACCTCGATCTCCTG +GGCTTAAGTGATCCCCCCACTCAGCCTCCTGAGTAGCTGGGACTACAGGTATGCATCACC +ACGCCTGGCTAATTTTTTTTTTTTTTTTTTTTTTTGAGGCAGAGTTTTGCTCTTGTTGCC +CAGGCTGGGGTACAATAGTGTCATCTCAGCTCACCACAACCTCTGCCTCCCAGGTTCAAG +CAATTCTCCTGCCTCAGCCTCTCAAATAGCTGGGATTACAGGCATGTGCCATCACATCCG +GCTACTGTTTTGTATTTTTAGTAGAGATGGGGTTTCTCCACGTTGGCCAGGCTGGTCTTG +AACTCCTGACCTCAGCTGATCCACCCACCTTGGGCTCCCAAAGTGCTGGGATTAAAGGCT +TGAGCCACCATGCCCGGCCCATGCCTGGCTAATTTTTTTTAATTTTTATTTTTGTAGAGA +TAGGGTCTCACTATGTTGTCCAGGCTAGTCTTGAACTCCTGGACTCAAGCGATCTTCCTG +TCTCAGCCTCCCAAAGTGCAGGAATTATAGGCATGAGCCACTTTGCCAGGCAAGGATTTT +TTTCTTTTTAAGTTACATTTCTGCCTGCCACCACAGCAGCTCTTTCTCCTGCTCTCTCTC +TCTCTCTGTGCTTTAAGATGATAGTCCCTTCTTTTTTTTCAAATAACCACAACAGGAAGG +ACTGACCACTCTTGTAAGCTGCAACTGATGTTTTCAGACTCCTAAAGTGACATCTAGACA +TAAGTCCATATATGTCAGAATATCATGCAGGGAATGCTCAAATAGTTGGGAAGAGATTGC +TGCACTGTGTTTTGCACGCCCAAAGCCCACATAGGTACTCAGTTTAAAAATCTTAATAGA +ATTGAATCCTGCTCTTATCATAGGAAAGGAAGAGCATCTGATAGAAACACAAAATGAAAA +GGTCAAGAACTGGCTGGGCACAGTGGCTCTCGCCTGTAATCCCAGCACTTTGGGAGGCTG +AGGCGGGAGGATCATGAGGTCAGGAGTTCGAGACCAGCCTGGTCAATATGGTGAAACCCC +GTCTCTACTAAAAATACAAAAAATAGCTGGGCGTGGTGGCGCGCACCTGTAGTCCCAGCT +ATTCAGGAGGCTGAGGCAGGAAAATCGCTTGAACCTGGGAGGCGGAGGTTGCAGTGAGCC +AAGATCACGCCACTGCACACCAGCCTGGGCAACAGAGCAAGACTCCGTCTCTCAAAAAAA +AAAAACAAAAAAAGTCGAGAACTGGAAAGGAACTAAGCGCATGAAAAGAAATTTTATGTT +CCTTCATGTTTTTATTTAAAGAAAGTGAATCAAGTACCAAACACGGAATAAAGGCAAACA +TTCATTTTTGGGGTGATTGTTCCCTTCTTGGCAATCCCTGTTTTATTGAGGGTATCACTA +GTTATTCAATCCAAGGATTTTTTTTGTTTCCACAGGAGGTGGGTGTTTCTTTGTCTTCTT +AGAGTCAGGATTCCAGATCTCCTGATGTGTGGGACTTTTCTTGGCCACTACGATTTCATC +TACAGTCACGAGCTGTAGCACCACCTCAGCCACTGCTCGAAATCCTTGGGCTTTGACTAT +TAGGGTGTCCCACACCCCTTCCTGGGCCACATTTATTATCCCTTCAGTTCCCACACCCAT +TAGGAGGTTCCCACCTTGGTGCACTCCACTCATTTCTGCCATCACGTCTGAGACAGCTAA +GCCTGCATTCTCTGCCAAAGTTTTAGGAAGATACTTCAGGGCCCAGGCAAATGCTAGGAA +TGCAGGCCCACTGGGCCCTTCCAATCTGCTTCCTTTATCAGAAAGCATTTTTGCCAAAGC +CATTTCTGTGGCCCCAGCTCCTGGAATCAGTCTGGGATCTTGACATAGCTGGAAATAGGC +ATCAATGCCGTGGTAGACGGCCTGCTCTGCACTCCGCAGCCCCTGGGTGGTGGCTCCCCT +GAGAACCACAGTGAGGGCAGGTGTGCCTGTACATTCCCATTCAAATACCACAGCCAAACC +ATCTCCCAGCTCCTGCCTGTAAACCCTCTGGCACTTGCCTGGCCTCTGGGGAGGGAGCAG +ACGAGGCAGCAGAGGTGTGTCCAACACCTCACTCAGGTAAATGATCTCCATCCAAGACCT +AGCTTGAATCACCACGATGCCATACTTGTCCGCCAGTGTGAGGGTCTCCTCGTCGACCTC +CCCCAACACCACTGCCACATTAATTCCTGCAGCTGCTAGCTGGCCTACTTGCTTTTCTAG +TAATTGATCGCTTCCTTTACTAAATTGAGCTAGATCAGCAGGACTAGAAAGACGGGCCGT +TGCTGGTGCATTTGGATGGGCAGGACCAAAGGGGCAAGCAAAGAGAGCCACCCTGGCACC +ACTTAACACTGTGGCCATTTGCCCACAGAGCTTCCCAGATATTGCTAACCCCGGGAGGAG +GCAGGAATCCTCCAGTGTCCCCCCGGGCAGCGCGCACACCCCAACACGCTCAGGCTTGAA +GCTGCCGTCTAGTTCCTTGATAGCCCAGCAGGCGTGGGCCACCAGCTTGGTCAAGTGGTC +CATGGGGGACAGGGTGTGGGTATTCATCACAGAATGGAGGGCCCAGGATGGATCTTCCAA +AGGCCCCAGAGATTGGATGGCCAGGGAGGGCAGTGTGGCCAGGACCTCTGCAGTGGCCGT +GGCGTAGGCCTCCCGGAGCTGCGGGCGAGGCAGGCCAGCCTTCAGCAGCTGCTCTGCCTG +TTCCAGCAAGGCTTCCGTCAGCAGAACCACGAAGGCTGTGCCGTCCCCACTATTCTCTGC +CTGGGTTTGTCCTGCTTCCCGGAGGAGCCATGCTGCTGGGTGCTCCAGCTCCAGGGCCCT +GAGGATGGCAGTGGCACACCCCGTGCACACTGTTTCTCCTTTCATGGTCACCAGGAACTT +CTGCCGGCCGTGGGGGCCATAGCAAGGCCGGATGACACTGGCCAGGGTCTGGACTGCAGC +CAAGCTGCTCAGCAGGTGGGGCTCCTCCTCTTCTGGACTCCTCGGGCTCTCCCTTGGGTT +CAGTGCCAGCCGCTGGGGCAGCTCCAGGGCTGAAGGGACTGTGCTGTCCATGGCCCGCAG +AGAGAGGAGAGGCCACCGTGGGTTGCAGAGATGCTCTAGAAACAGCAGCTGGGGCACTCC +TGACACCGATCGTTGAAAGTACTCAAGAGGTCAGTGGAAGCAAGGAGCCAAATGCCCATT +GATTGGTATCTGAAGACATCAGCACGGACCAGCACTCCACTGTGGGTCCAAGGATGAGCT +CCAAAGAGCCCAGTCCTAAAGCCACCCCAGGGTTGATTCTGTAAAGGAACTGGGTCTTGG +GGCCTCTCAACCTTGGTGGCTGAAATGGGATCTTTAACTGATGAAGTCACAAAGTGGAAA +ATGGAACCAGGATAGAGAATGAGGTCACAGAAGGCTGGTTAGAACTGAGGAGGCCCTACC +AGCAGGCAAAAGTCAGGCCTTGTCCAGCAATGGAGGTACATGCACCTCTGCACCAGGTTT +GAGACTTGTTTAAACGTAAGAGACAATGAGGAGGAGATCAAGTGAAAAACTACCCATTTC +ACCCTATCTGGAGTGCAGGGGCATAACCATGGTTCACTGCAGGCCCAGCTCCCTGGTCTC +AAGCAGTCCTCCTGCTCAGGTTCCCAAGTACCTGGGACTACAGGCACACACCACCACACC +TAGCTAGTTTTTTTATTTTTTGTAGAGACAGTGTTTCTGTCTGTTGTCCAGGCAGGTCTC +GAATTCCTAGCCTCAAGAGAGCCTTCCACCTTGGCCTCCCAAAGTGCTAGGACTACAGGT +GTGAGCCACCACCTCACCCACCCTTTTTTTTTTTTTTTTTTTGAGACAGAGTCACACTCT +GTTGCCCAGGCTGGAGTGCAGTGGTACAATCTTAGCTCACTGCAACCTCCACCTCCCAGG +TTCAAGCAGTTCTCCTGCCTCAGCCTCTCAGTAGCTGGGATTACAGGTGCCAGCCACCAC +GCCCGGCTAATTTTTTATATTTTTAGTAGAGATAGGGGGATTTCACCATGTTGGCCATGG +TTGGCCAGGTTAGTCTCAAACTCCTGGCCTCAAGTGATCCGCCCACCTCGGCCTCCAAAA +GTGCTGGGATTACAGGTGTGAGCCACTGCACCTGGCCTTTTTTTTTTATTTGAGAAGGAA +CTGAGAGATGATGTCTGTGTTTTGTTTTGTTTTGGTGTTACTTTCTCTTGCAGTACTGTG +TAATATTAGCCATGTTTTGCTGTCTGCCTTTGACTTTTTGGGTATCTTATCAGTTTGTGC +TTGTGTATCAGGTTTCTTAGGGTGTCTGTTGGTCTTTCAGGGTGCAGGTGTGGGAGGCTG +CACAGCGTGCATGCCTGTGCCACGACTCCCAACTCTGCCTCCCTGGCAGAGGCAGGGCAA +GACAAGTGGGGAAGGATGCTGACAGCTCACAGACAAATAGAAGTGAACCCAGAGGGGTGA +AAAGCAACCAGCCTCCCAGCGGTCAGGGAGGTAGAAGCCTAAATGGGGTCCTGAGATTTA +AATGCGAATCGCCTTCCCATCCTAACCTTCAATGCTTACAATTTAAGTCTCTTTTTTTCA +TTCTCTCTCCTTTCCTCACTTGTCTCCTCTTTCCTCCTATAGAGCCTACTCGGGTAATGA +TGCTTCTGCTTTAGTTTAACACATATTTAGTCTGGGCGTGGTGGCTCATGCATGTAATCC +CTGCACGTTGGGAGGCTGAGGCGGGAGGATTGCTTAAGCTCAGGAGGTTGAGGCTTCAGT +GAGCCATGATTGCACCACTGCATTCCAGCTAGGGCAACAGAGTGAGACTTGTCTCAAAAA +AAATAGGGGAAAGGTCATTTGGAATCCTAGTCCAGAGATAACCATTGTTTACAACTTGAT +GAACATTACTACTTTGCACATATTATATGCATACATAATTATAGATTTACACCATTTTAC +ATAAGATTATGATACATATATGCTATTCTGTGATCATTTCCCCCTCAACATTATCTTGGC +TCAGAGAAATGTTTCTTTTTTTGTTTGGACATGGAGTTTCGGAGTTTCGCTCTTGTCGCC +CAGGCTGGAGTACAATGGCGCAATCTCGGCTCACCCTCGGCTCACCACAGCCTCTGCCTC +CCGGGTTCAAGCAATTCTCTTGCCTCAGCCTCCTGAGTAGCTGGGACTGAGTAGCCATGT +GCCACCATGCCCGGCTAATTTTGTGTTTTTAGTAGAGACAGGGTTTCTCCATGTTAGTCA +GGCTGGTCTCAAACTCCTGACCTCAGGGGATCCACCCGCCTCGGCCTCCCAAAAGTGCTG +GGATTACAGGCGTGTGCCACTGTGCCTGGTCTGTGAGCCACTGTGCCCGGCCTGAGAAAT +GTTTCTTTTTTTCTTTCTTTTTTTTTTTTTAAGCAGAAACACATTCATTTATTAACCAAA +GGGATGATCCTAATGAATCCAACACACTTTGAAATAGCTGCATGTAAAATGTTTGTGATA +AAGATAATTGAACACAGTAATGAAAAAAAAAAAAGAAAGAAAGAAACGGTATGGAGATTT +GCTCATTGAACTGAGCTTGGTCATTCTCTTAGTTAACTCCTGTCCAAAGTGATGATGGAA +TCTTTATTGTACTTTTTCATAGATCCGAGTACAGGCGACATGGTTCATGACACAGTCCAC +CACTAATTTCCCATCTTTCAATGTTCTTGTTATTGTGCTTTCCTTCCCATCCCACTCCTG +ATGCTGAACCAATGCACCATCTGTAAAGTTGCACACAGTCTGAGTTTTTCTGCCATCAGC +TGTGGTTTCTTCAAACTTCTCTCCCAGGGTACAAGAAAACTGTGTTGTTTTCAAAGTGCT +CTCAGTTTTTATGGTGAGGTTTTTGCCATCACAAGTGATGATACAATCTGGCTTGGCCAT +TGCGCCCATTTTTTGCAAAGCTATTTCCTCCTAGCTCCTTCATGTATTCATCAAAGCCTT +CGCTGTCCACCAGGCGCCATCTTCCTTCCAGCTGCTGAACTGTGGCCATGGTGGGTGCAG +GGGGGCTGGTGTGCAGAGCAGGGTCTGCGTCGGCGTGGCAGCGTGCTGTCGAGAAATGTT +TCTAAGGAGATCTTATTTGGTCTGAGAACCATGAATGATTATTTTGAGCACTTTTGATTC +TGGAGACTCCATTTGGATCAGGCATGGTCCTCCAAATTCAGGCTTCTGAAAGCCTGTACC +TCAGAGTAGGCTTGATGTTCCATAAAAGATGTGGTTATGAGTGCAAAGATGACTTGCCTG +TATTGTTATACAAATGTAAAATGTAACAATCAACAAAAATGTAGCAAAGTATGCATGTAT +ACATTTTCTCTAAAGATACAGTTTCTTTTTTGAAAAAATAAACACATTAGGCAGGTGTGA +TGGCGGGTGCCTGTTATCCCAGCTACTCCGGAGGCTAAGGCACGAGAATCTCTTGAACCT +GGGAGGTGGACAAATTGCAGTGAGCCAAGATTGCGCCACTATACTCCAGCCTGGGCAATA +GAGCGAGACTCAGTCTCAAAAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAA +TAAACACTACCGGCCAGTGGCCATGGCTCGAGCCTATAATCCCAGCACTTTGGGAGGCCT +GAGCCAGGTGGAGTTCAGGCATTCAAGACCAGCTTGGGCAATATGACAAGACCCCTGTCT +CTACTAAAAATACAAAACAATAGCCGGCCGTGGTGGTGTGTGCCTGTAGTCAGCTGCTTG +GGAGGCTGAGGTGGGAGGATTGCTTGAGCCCTGAAGGTGGAAGTTGCAGTGAGCTGAGAT +AGTGCCATTGCACTCCAGCCTGGGTGACAGAGTGAGACCCTGTCTCAAAAAATAAAATAA +AATAAACACTCCTATAAAGGATCCTCTTAGCTCTTTTTCTAACACCTAATCTACATTTTC +ATATTCATTTCAGTTACCCTACAACTGTTCACTGAGCTGCTGTTGAATAGGGGAAATAAG +GCAGATAACTACTGCCATCTCCGCTGGAGGGACGATACAGACATTAATCTGGGCACTTTG +ATTACAGGCAATGAGAGCTGTGAGTGGGGAAAGCACAAGGTTGGCAGAAGCATTTAGGGG +GACACAGCCATTCTCACGGAGGGCAGAGGTCTAAAGCAAGAGCTGAATAAAAAGTAGGAA +CTGGCCTCGTGGAAAGGGGAAGGGTGATGGGACAGCCTGGTGGTTTGTAGCCCACTGGAA +GGAGTTCTGAAAACTGGTGGTCAGGTGAGAAGGAAAGCTGGGGAAGAGATGAGCACGTTC +GCCAGAGGGTAGCAGGGGCTCTCCGGACCTAGTGAGTCAAGCCAAGGAATTAAGGCTTCA +GCCTGCAGGGTGATGAATAGGGCTGTCTATTCCATTTCTTCCTTCTTTCTTTCTTTTCTT +TCTTTTTTTGAGACAGCGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGGCACGATCCT +GGCTCACTGCAACCTCTGCCTCCCTGATTCAAGCAATTCTCCTGCTTCAGCCTCCAGAAT +AGCCGGGATTACGGGTGCCTGCTACCACGCCTGGCTAATTTTGTATTTTTAGTAGAGGCG +AGGTTTCACCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCAAGTGATCTGCCTACC +TCGGCCTCCCAAAGTGCTGGGATTACAGGTGTAAACCACCGTGCCTGGCCTGAAAATTTC +TAGTTTATGATACTTGCCAGCAGAATGTGTTCTGTCACCCTCTTCTGAATAGATATGGTT +GTCTGCTATGACTTCTCCCACTGCTGCCCTTCCCCCTGAATCCACAGATGCATTTCTTTT +AAAACTATGATCTTGTACACAATGGATGTAAATATTTAATCTTTCTATTTGTATGTTTTT +CCATGTTTCTTTTCTTTCTTTCTCTTTTTTTTTTTTTTTTTTTTTTTTTTGGAGGTGGTG +TCTGCCTCTATTGCCCACAGGCTGGAGTGCACTGGTACAATCTCGGCTCACTGCACCCTC +CGCCTCCTAGGTTCAAGGGATTCTGCTGCCTGAGCCTCCTGAGTAGCTGGGACTACAGGT +GTGCACCACCACGCCCGGCTAGTTTTTATATTTTTAACAGAGACAGGGTTTCACCATATT +GGCCAGGCTGGTCTCGAACTCCTGACCTCGTGATCCTCTCACCTCGTCCTCCCAAAGTGC +TGGGATTACAGGCATGAGCCACCGTGCCCGGCCTCCATGTTTATTTTCTAGTTGCTTACT +TGTCCTTTTGTGTTTATCCTTGTTAACTACTACTGCCAGGCTTAAAGTATAGACCCCTAG +AGGGCAAGATTTGTATCTATATAAAATGTACTGCAAAACATCTACTTAAGCCTCACATTC +TTAAACACAAATTACTTTTGAAGATGACTGTTCTGTTTGTTTCCTTCCTGGTTTCTTCCT +TTAACTTTTCCACCAAACAGGTACATGATATACTTTACTGAAATAACTTATATAGCAATA +TGAATTTTTTTTTTGAGGCGGAGTTTCGCTCTTGTTGCCCAGGCTAGAGTGCAATGGCGT +GATCTTGGCTCACTGCAACCTCCGCCTCCTGGGTTCAAACAATTCTCCTGTCTCAGCCTC +CAGAATAGCGGGGATTACAGGCGCACACCACCATGCCAGGCTAATTTTTGTATTTTTAGT +AGAGACGGGGGTTCACCATGTTGGCCACGCTGGTCTCGAACTCCTGACCTCAGGTGATCC +GCCTGCCTTGGCCTCCCAAAGTGCTGGGACTACAGGCATGAGCCACCGTGCCCGGCAAAT +TTGAGGTGGAGGTTGCAGTGAGCTGAGATCGCATCACTGCACTCTAGCCTAGGTGACAGA +GCAAGACTGTCTCCCACTTCAGCCTCCCAAGTAGCTGGGACTACAAGCATGTGCCACCAG +ACCTGGTTAATTTTTTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCCATCACCCAGGCT +GGAGTGCAGTGGCGCGATCTCAGCTCACTGCAAGCTCCCCCTCCCGGGTACACGCCACTC +TCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCACCTGCCAGCACGCCCGGCTAAC +TTTTTGCATTTTTAGTAGAGACAGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCC +TGACCTCATGATCCACCTGCCTTGGCCTCTCAAAGTGCTGGGATTATAGGCGTGAGCCAC +CGCGCCCAGCCAGGCCTGGTTAATTTTCTTTGGTATTTTTTTGTAGAGACGGAGGTCTCA +CTATGTTGCCCAGGCTGGTCTCGAACTCCTGAGCTCAAGTGATCCACCTGCCTTGGCCTT +CCAAAGTGCTAGGATTACAGGCATGAGCCACGGTGCCCAGCCTACAGTGCAACTTTAATA +ATAACAATATGAACACAAAAATTCTAAGATCTAAAATTTAAGCTTTCAGTAGTCCTTCTA +TAACTGTGAAAGTTTGGTTCCTAAAAAGCCCTGAGGAATTTATGGGAAAACAAGAGAGAC +AACATTTAGTAGTGAACCTGTGCATTCTAAATAAAGACAATATCAATGACGTGTTATAGG +TCTTCAATTAGTAAGAATGAATATTGGACTATGAATTTTTATTCACTGTCACTTGTTTGC +TAGATGCTTTGAGAATCTTCCTTGCCTATATTTTCCTGAGATGTTGGTTTTTCTTTGTCA +CAGATAACAATGCTCATTCCCTCCCCATTAAAAACTAAATATATATATATATATATATAT +GATTAAACGATTACTACATGTGCTTTGAAATATTCAAATATTTTAGACAGTAAAAGTCCC +TTGTAATTCAACCCTTTGCAGATGATTGGTTAACAGGTTAGTACACATCTACCTAAATTT +AAAATCCCATATTTAACATGTATACTTATTAGAAAGTACACATTCTAATATTTTTCTATT +GTATTTGGTACTATTTTCAGATGCTCCTGCCTTTTTCTTTCGTAATTTTGAAGGACCTCA +GCTCCCTGCCTCCTAGATTTTTGCTACTATGGTCTCAGAGCTGTGTAATTTGGATGACTG +AGATGGAAAAACCTCTGGAAAACCTTTATTTATGTTGAATAAGTATTCCTTGAATCCTTC +CTCAGCATCCTGGGTTATATTTGATTTGCTCTGCTCATGATAACTTCATGCCAAGGAGAC +TGCTATCAGTTCTCTTAAAACAGATCCCAACTCCCTGCTCATAGTGGCCAAAGGAATGGA +GATTTCAGGCTGAGTTTACTTACGTGCATCATCTTCATCTATCCAGAAGCATCCCTGCAC +AAAACCTCTGTTTCTACCCTTCCATTCACTCGGCTCACTTTTCTGCTCTTAGTACCCTTT +GTTTCTTGTGAACTCTCCAGCAGGAGTGACTTGCAATTTGTATCCACTGACACTTAAGTT +CTCGGAAGTGCTGGAGAAGTGTATGGAAGTAAATTATCCTGATGTATAATTTTGTGCATG +TGAAACTCACCGTGGAAGTGCCTATCTAATTTCAGTATGGAACACAGCTAAACATTTGGA +TCAATAATCCAGTTTTGAAACCACACTTCATTTAAAGTACAATGTGCTGAAAAAAATGAA +AAAAGGGTGCTTTCAAATTTGTACTTAGTAAACTTTCACTAGATCACATCATATGTTTAT +CACTAGTCATGTTGTATTTCTATGTGTAATCGCCAGGCACTTTTAATTTCTAGTTTGCAT +TTACCATGCCAGCCTCCTCCTCAATCCCAAATTTCCTTTGGTTATAAATTTAGTAAATTT +GAAAGAGCCAGCAGGGATTAAACCCTGAAGGTATTCAAATGACTATCTGACGTTATTCCT +CATTTCAGCCATTTCGAAAAATTATGCTTTCATTTAGAATAGGCTCTGGGAATCAAAGTG +TGTGTATTTTGCCCAAGTAGAAGACACAGTTTAAAGTTAACATCCTAGCTACTAGAAGGG +AAAGCAAACAACATCGCTGCAAAAGGAGCCTATTTTTTTTTTACCTTACACTAAAACTAC +ATTGTGAAGATCAAACGAAATCAAGATGAGAGTGTGCCTCTTAACGCCAGGTCCAAAGTA +GATGCTTATTAAATGATAGTTTACCCCAATCCTTCACAAATGGTTGATAGGTCTTACTAT +TTCCCCCCTATTCAAATCTAGAATTTTTTCACTCCCATATACTAATCGATAGTTAATGGA +AAGCACAGAATAGATCATCGTCCAAGTGTTAGGTATTAGCCTGAGGAATCCGGAATCCCA +TATTTGTAACTGTCCTTCTTGAGAAAGTGCATTTTTCAGGCGGATTCTAGCCCCATTTTT +CCTTTTACCATTTTTACATGTTATGAGAGGTGGCTTAGAAATACTTCGATTTTTGCCTCT +TCATCACAACACACTGAACGTTAAAATCAAGTGGTTGGGTTTTTATTGGCTTATTTTGTC +TCTAACCGTTTTATTTCTCGAGCTGTCATCGTTCTTTTCGTCTTACATCCTTATGAACCT +TTTCTGGATTAAAAAAATGACGTTATAATAAGGAAACTGTAACTGGCGTTGGATTAGAAC +GAAGTTGACTCCATTCCTTTTCCTCCCCGTAGTGTGGGCGATACGAGGAAAGACCTCGGC +AAGAACCAGCGAAGCCCCGGCTGCCCTCGCCCTGCGGGCGCACACTTGCTCCTCGCGCCG +GGCTGCGCCGGGCGCCCGCGCCGCCTCGGCGTGTGTCCGCGGCTCCCTCCCGCCCTCGCC +CGCAGTCCCCCGATCCCGATCCCGGATCTCTGGGTCCACAGCTTGGCTCCCTCCCGAGCC +GGAGCCGGAGCCGGAGCCGAAGTCGCGGCTGGGCCCGGCCGCCCCGTCACAGGGGGAGGG +AACCCATGGGGAGGGGGAGGGGCGGTGAGGTCAGCGGCGGCGGCGCGTCCGCGGGCGGCG +GGAGCTTCGCATGCGCGGAGCGAGGCCCGTGAGTGGCAGCGGCGGCGCGCGGGGGGCGGG +CGAGGGGCCGAGAGTGGGGGAGCGGGCGGGGGCCGTCGAGGAGGCGTTGTGTGGGCGCGA +CGGCTGCGAGTTGGGGAGGTCTGTGGTGCGGGTCGCCCCGGGGGATCCCCGGCGCGGGCC +TCGCGCGACGGCCACGGTCGCGCGGCGTGTGTGGGGGGTCCACGCACACCCGCAAAACTT +CCTCCTCCCCTGCTCCGGGAGAGCGAGCGAGCGTGTGTGAGAGCGAGTGTGAGGAGCGAG +CCGCGGCCCGACGCCCAGCGCCGCCGCTGGAGCAGCTGTCAAAACTTCGCCGCCGCCCGG +GCCCCGCGGCCCGCCCTCCCCGCGCCGGGCCCCTTTCTCTTCCTGCTGCGGGCGGCCCGG +GGGAGGGGCCGCGGGCGGAGACCCCGGAGGCCGGCGCCCCTCACGCCGCCCGCCCGCCCG +CTCCCCGCCCGGCCCCTGCGCGCGTGCGTGTCCTGCTCGCTCCATGTTGCCGCCTCTCCC +GGTACCTGCTGCTGCTCCCGGGGCTTCGGGAAATGCGAGAGTCTGAGCCGGGGAGGAGGA +ACCCGAGCAGCGGCGGCGGCGGCCGCGGCGGCGGGAGCCCCCCAAGAGGAGGACCGGGAT +CCATGTGTCTTTCCTGGTGACTAGGATGTCGTCGGAGGAGAACAAGTGCGTGGAGCAGCC +GCAGCCACCACCCCCCGAGGAGCCTGGAGCCCCGGCCCCGAGCCCCCCAGCCGCAGACAA +AAGACCTCGGGGCCGGCCTCGCAAGGCGCTTCCCCTTTCCAGAGAGCCAGAAAGAAGTAA +GTTGAGTGCGAGGGAGCCAGGCCGGGAGCCAGCGGCGGCGCCGGGCCGGAGCTGCCACCG +GGCGCCCGCCCCGCGGCCTCCACGCCTTGGCGCCCCCCGGCGGGATGGGGGCGGGGCGGG +CCCGCGGGCGGCGGCAGCTCCCGGCCCCGGCCCCACGCCCCTCGGTAGCCGCCCGCGCCC +GGCCTCCCCCGCTCCGCGCCGCCCGCCCGGGCTCCCGTCGGCGCCCGGCTTCGCACACTT +TACTTTTCAGTCGGGCCTTTTCAGTGGGTCTTCTCCGCGACTCTTCTTTTGGAGAAATTT +CTCGTAGCCGCGTCTTGGCCTAGCTGGATCATTGAGAAAACAAGCCCGGAGCGCGCGCAG +GTAGTCCCCGGACGGACTCCGAGCGAACCGCCGAGCCGTGGGCGCTCGGGAAACTCGGAG +CTGTCAAAACGCCCGGGCCAGGTGGTCTCGGGGCGCGGGCTGGGGGCGAGAAGAAAGCGG +CCGGGCGAGTGCAGCTTTTGTTTGTCAGCGACTCGTTCGTGGAACTTTTCCTGGTCCCAA +ACCTGTGTTTTCTTCTTTTGATGATATATTAGGAAGCCATTTGGCTTCTTCCTTCCCCCT +CCCCCAACACCCAGCACCGCACTCCCGGGCTCCGAAAGCACAAGTCCTGTGGGAACCCCC +AGCTTCGGGGAACGGCCTGCCTAAGTTTTGGAGACGTAGCCAGCGTCCCCTCGTAAGGCA +GAATACCAAGAGCACTTATTCAGAGAGAGTGCAGATGTAAATGTCGTTTCCCTCGTAAGT +CTTAGCTGTAAGGGGCTTGGGAATAGGGTCGCCTGCCTTTGACCGACCGTACTGTAGGGC +TGGACACCGGCTTATTAGAGGACCAGAAATGTCTTCTTACAGAACGGTTATTTGACGGCT +TTGCTTGTAAATTAAGACACCGTTTTAGTGCCAGCGAGCTGCTCGGCTTCTGTGGCTCTC +GCGTGTGCCGTGGAAGAACTGTGAATGTCTTTCGAAGTTGTAGAATGGCGTGTGTGCTTA +CTCATTTCATGAGATGATATTCTCATTGAACTGTCGGGAGTGGAAGGGTGCGCTGGGACG +TGAAGGAAGCCAGCACGTTTATGGATAGGCTGTTTCTTTGGTTCGGGTGCATTCACTTAG +TAATAGTGTTGTTTGGTGATTTGTAGTAAAAATAGTAGCGTGAACTGAGGCATAGCAGAG +CTGGGTTGTGGGAACCCATTAAGCTCTTGACTTGAATGTGCTCTTTTCTTGCCCCGCTGT +CCTTTTACTATGAAAATGATTCAGGGCCTTCAACTTGCCTCCATATTTTATTGCCAGCTC +TTACCTAGCTATGATAATCGTGAGGGAGGCAAGTACAGGATGTGTGTACGTTATTACATT +AGCTTCTTCGTGATACAAAGTTAGGACTTACTTATGCCACTTGCGTTGTAATACAATGGC +AAATATAAAATGCCCTTATTCTATATTAACTGAAATTTGGAGAAGGAAGTGGAGGTTTAA +GTAATTTTTAGACGTCTAAGCCACTTTTTTGCATCCTTTAAAGCAACTCAGGACAAGCCA +TATTGGGGGTTTTACCTTGATTGCCTCCCATTTCACTATTTGCAAAGCATTTCTTCATCT +CTTACTGAACATTAATTTGCAATTTTTTTTTTTAATTTGCATTTGAATTCTTACTCCAGA +AAGATTAGATCTGTGTTGTCACACCCCACACCCCATACTCCTGTAAGGGCGTGCTTGTGC +ACGCGCACACGCTCACACGCACGCGCACACTCGCACACACCCTACTTTTGAAATGAGCTC +ATTTGTATTAGTGCAGCTCCTGAGTGCACTGGACGATTAGGGTATTGCCACTTTATTATT +TTAATTCTTAATCTCATATTATGAAGAAATAGGTAGCCTTTGGAGAAGATAAAAAATTTC +TGCTGAATAACAGTATAATCTAACTATGAAACATCAAAACTTTTGGAAATATTTAGAACA +AATGTAAGTCTGTAGAGAGCTTTTTCTTTTAGATTTGAAAACTAGTACTGCTTTCTTTAT +AGGAAAGTAAAGTCTACTGGTAAATTTCACGGGTCTAAACTTTTTAGAGCTTTTTTTTGA +AATTGTGTCTTTTGAAGGGAGTGGAATCTCCAGTTGTTTTTAGAAACATGTAAATGGAAA +CTAACATATGAATTGGAAAGCAAAGAGAAAGTTTTTCAATTGTGTATCTCTATACTGTAT +AAGAATCCATGCAGAAAAGACCCTGTAGTTGGATAGTAAAGACCCTGAAGGTGAAACTTA +TGTGTAACCAGTGTAAATTAGGTTTGTAACCAGTGAAATTATGTGAAATTGCAAATAATT +CACCTGAGAAATGAAAATTAATCTTCTTTGCTAAATGCCATAGAGATATTTTAAGTTGCT +AATGTTACTTAGATGTTCATTAACTTAGTGAGTTACATTAAGTAGAGAAGATGCCTTTTT +TTTTTTTCTGTACGAAGTCTTGCTCTGTAGCCCAGTGTAGTGGTATGATCTCGGCTCACC +ACAACCTCCGCCTCCTGTATTCAAGCGACTCTCCTGCCTCAGCCTCCAGAGTAGCTGGGA +TTACAGGTGTGCACCATCGCACCTAGCTAATTTTTTGTATTTTTAGCAGAGACAGCATTT +CACCATGTTGGCCAGGCTGTTCTTGAACCCCCGACCTCAGGTAATCCACCCTCCTTAGCC +TCCCAAAGTGCCAGGATTACAGGCGTGAGCCACTGCACCCTGCTGAGAAGATGCCTTTTG +ACAATGAAGTGGATTTGTATATTTATCTTTGGCTTAAAAAAACATGCACCACCAATTACA +CTTTCCTCAAGTTTAAATTTTTAATAATTAGGAAAATAAAGCATTTTCTTGTCTTATAGT +GTTAGCTAGATTGTTTTTGTGTATTTTGTCATGAATAAAAAGCATAGCTATATAGTTACT +GCTTTTACATTAACTATAAATATCTTAAAATTTTACTACCTAAAATCAGGAAACTTGAAC +TGAAGCTACTAATCTTAGAGTTGGAAAAGTAAATACATAGAGGTTTCCTGTTGTACAAAT +GTCAAGTGGCACAGTGAAATTTACATTCATTTGAAAGTTTTCCTTAACTGTAAAAAGTAT +CAAATTACTTGATACTTTGGAGTAGTTCATCATCTTTATCAGAGGCACAGGTCTTAACCA +TTGGCAAGCCTCTGTCAGAATATGCACATATTAAAGATCTGATTATTTTTGTGTTAATGT +TAAAAAATTTTTCTGAAGCTTTTATCTTATTTTTTCCATCCTTACACCGTAAATTCACAT +TACCAAGTTGGGAAGCCAAAGAAACATTCTACTCTACTATGTTTCTTACCAGTTCATGAA +AGTTGATGTTAGAAATGGGTGTGGGTGTGGGGGATGGGGGTGGTTGTACAGAAGCAGCAG +GTGGTAGGGATAGGATTTCTGAAGCACTATCCTTGGCCTTTTTTGAGTAAACTCTTTATA +CCCTGAGCCACTTTCTTTTCAGAGGGCAATTGCTATTATTAGAGAGCCACCTTAAGCATT +ATTGTTGTAGAAAAATTAGGCACAACCAGTGATTGTCATTACAAGGACCAGCAAAAATGG +CTAGGTTGCTACTCTGTATTTGTAACGCCCTTCCCCCAACAAAATTTCTCCTTTTCATAT +CTGTGAATTAGAAATAAGTGATAGAAAACTGTACTGCATTACAATATATACCATTTAATA +AAACAAGTTTATAGTTGAGAGCACTATTCATGCTTTTTGAGATAATGCAAATTTGTAATT +TTTATGATAGCAATTCTTAATAATTTATTGTCCAAGAGATTTGATAAAATTTTTGATAGT +TATTGGTCTCTGGGACTCAATAGGCACTGAAATGTTTTAATTCAGTTGAAAAGTTGGTTC +AGGATTGCTACCCTCTCTTACCTGTTAGGAGGTTGTTGTTTAACCTGACCTGAAATTCCC +ATGAATAAGAACCTGTTTTTTTTTTTTTTTTCTTTGACAGAGTCTTGCTCTGTCGCCCAG +GCTGCAGTGCAGTGGTGCGATCTTGGCTCGCTGCAAGTTCCGCCTCCCAGGTTCAAGCGA +TTCTCCTGTCTCAGCCTCCCAAGTAGCTGGAGTAGCTGGGACTGCAGGCACGTACCACCA +TGCCTGACTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGG +TCGCAATCTCTTGACCTCATGATCTGCCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAG +GTGTGAGCCACCGCACCTGGCCCAGGGAATTTCTAATATTTGAGAAGATGTTATTTTTAG +TCTATTATACAAATTTATATATTGTTTACTAATATATAAATTTACATATTGGTTACTAAT +ATGTAAACACCAATTTACATATTGGTTACTAATATGTAAACTTGATAAACATGGATTTCC +ATGGAAATTTAAAAGTATCACAACAATTTGTTTTCCCATTCTGAAACTTGTGATTTATTA +CATTTTCCTACTATTTCAGTTAATTCCATAATGCCAGATTTGTTGTCAATTTGCCGAGTG +ACAAGCCACACTGCTTCCTCTCATTCCTCTATTCCGCAAAACTGCAAAGTTTCCCAGACC +ACAGTCAGGTTTCTCTGGGTTGTCCAACTCTGTAAACTTACAGAGTGGTTGTCCAACTCT +GTAAACTTACAGAGTGGTTGTCCAACTCTGTAAACTTACAGAGTGGTTGTCCAACTCTGT +AAACTTAAGTCACTTTAAGTTTATGACGGAGGGGCTTCGTGAAACTTCATTGACCTTCCA +AGGTGAAAATTGGTCAGTTTTCAGTTATAAAGGACATTAAGGATGGGTGTGGTGGCTGAT +ACATGTAATCCCAGCACTTTCGGGAGACTGAGTCAGGAGGATCACTTAATCCTCATTTAA +AAGGAGTTTGAGACCAGCCTGGGCAACAAAGTGAGGCCTTGTCTCTACAAAAAAATTAGC +TGGGTGTGGTGGTAGGCACTTGTAATCCCAACTACTCTGGAGACTGAGCTGAGAGAAGAT +TGTGTGAGGCTTGGAGGTTGAGGCTGCAGTGAACGGACATCACACCACTACACTCTAGTC +AGGTGACAGAGCAAGACTCTAAATAAATAGGAACATTAGATGGTCTCTCTGCACTCTTGC +CTGGTGGGGACGTGTTAGATACCCTCGTTAGGTTGTGATTTAGTTTTTAATCTGTGAGAT +GTTTGGGTCAAACAATTTTTAGCTGCCATGGAATAAACTTTCCAGTCAGCGTGTGAGTTT +GTGTTTGCCTTTACTTTTTTTTTTCTATATTGTTTTGGTCTATTTTTATCTTTTAATTTC +AGAAAGCTGATTAATCTCTTCCTTTTCTCTTTAAAAATTTTCTTTATCATGTTTGTGCTA +CAGTGGTTATTTTGAGAACTTGTTGGCAGGATAAGTTGCAAAAGTTATGAAGTAGAATAG +GGATGATTTCTGTTTTTGTTTTTTTTTTTTTCAGACAGAGTCTCACTCTCTTGCCTAGGC +TGGAGTGCAGTGGCGTGATCCTGGCTCACTGCAGCCGCCGCCCTCCGGATTCAAGTGATT +TGCCTGGCTCAGCCTCCCAAAAAGCTGGGATTACAGGTGCATGCCACCACACCCAGCTAA +TTTTTGTGTTTTTAGTAGAGATGGGTGTTCACCATGTTGGCCAGGCTGGTCTCAAACTCC +TGACCTCAGGTGATCTGCCTGCCTCCGCACTCCCAAAGTGCTGGGATTACAGACGTGAGC +CACCATGCCTGGCTGAGATTATTTCTTTTTTTATTATAGCCATTGCTTGTAGATATATGC +TGGTGGTTATCTGTAAAAATGTAATAGAAAGGCCGGGCACGGTGGCTCACACCGGTAATC +CCAGCACTTTGGGAGGCTGAGGTGGGCGGATCACAAGGTCAGGAGTGGGAGACCAGCCTG +GCCAATATGGTGAAACCCCGTCTCTACCAAAAATACAAAAATTAGCTGGGCATAGTGGCG +GGCACCTATAGTCCCAGTGACTCGGGAAGCTGAGGCAGGACAATCGCTTGAACCCAGGAG +GCAGAGGTTGCAGTGAGCTGAGATCGTGCTATTATTGCACACCAGCCTGGGCGACAGAGT +GAGACTCCGTCTCAAAAAGAAAAAAGTAATAGACCAATCTTGAATTTATAATTGGAAGTG +TTGATCCCTTTATTTGCAGAATTTATTTATTTGTGACGCAGCTGTTGCTACCTCGCCTTT +TCTTTTGTTGAGCTTAATCTCATGTCAAGTCATTCAACCAACTCAAAAGCGATGAAGACA +TTATTGAATCAACCTGAACTAAATCAGACCTAGGCTTCTTAAAATATACAGCTTAATGCT +TCCAAATGATTTAGAAAACTAAAAAACCTAGCTACGCTGTAGGACACACAGTGGCCAATA +ATACAGGACCCCCAAACTGGCCAGTGGACCACTGCAACCACTATTTACTTCCTCCGTGTT +TAGGAATGTTCAACGCTCCAAGCCCCATAGGCTGATTCAAGAAGATAAAGTGAGACTCAA +GGAATTTCGAAGTGGAACAATACACCAAAGCCTTAAACCTGAAATGACTCTCCTTTTCTG +GGGGGTGAGGGGGAAAGAAAAAGAAAAAGTTTCTAGGGCTCTCGGGGTGGCCTGGATGCC +AGGGTCCCAGAAGTGGCCTTTTCTAGCTCCTGTAACTAAACCTGGCGGAAAACTCCCCGC +CTGCTCACTCCACCCCCACCCGCCCAAGAATGCGTCTTCCCGTCTTCGGTGGCCCTACCC +AGAATCCCAAAATGTGGGTTCCAACCCGGGCCCTGAATGTCTTCTCAAATCCCCGGGACC +CAGGTTCCGGTGCGTGCCTTGCGTGCCGGGTCTTGCCCCTCGGGCGGTACCACCCAGGCA +GCCCTAAATCCAGCCTCCCGGGCCCCCAGCAGCGCCCTCCGCCCCTCCACTATCCGGTCC +GGCTCGAAGTCGGGGCCAAATCCAGAGACAAGAGGGCTGTGCCTGAAACTGAGCAGTTTC +ACCACTCGGCACTCCTGGCGGAAACTTCCCTTTAAAAAAAAGAAAAGAAAAGAAAAGCAA +CAGCACTTTTGGGCTAGCATTTCAATCCTTCCTGCCCTTTAGAGTTCCCAGTTCTGCTTC +CAGCTGGCTTTGGGTGTTCCACTAGAATTGAGTTGTAAAGATATTCTTTAAGTGTTTATA +GAACATTAAGACTTAAAAAAAATCTTTAAAATTAGAGGAGGGAAAAAGCCACCTTATCGC +ACACATCCAGGAAATGCAGCCCCGTGCATCCCTGCTCAGGGATGAGCAGGCGCCCCAGGA +CTCCCGGAGACAGATTTTTGGGCACCCGAGGGAGTCACCGGGCGCGTGTCGGGGTCCGCG +GTGAGGCCCAGCCCCTCCGGCGGTCCCTTAGACGCGCCCTCTGCCCGGCCGGTGTGGACC +GTCCCGGCCATTGTTTACGGGGGATGCCCGTCCAGACGCATTGTTTTGGCCGTTTCCAAC +TTGCCCCGGCCCTTTCCGGGGCATCGCGGGGGACCCTACACCGACGTCCCCCCTCCGCCC +GCGCCCCAAGGGCTGACTGGGCAAATTGGCAGATCCGCCCCGCGGGGCGACCCAACTTTT +CGGAACAGCCCCCCACCGCCCACCCCTGCAGATCCCCGGACCCCCGCTCCCGGCGGAGAT +TCAGGGAACCCCGCATCCCAAGCCCTTCTAAATCGTGCGGCCTGAGTGTGACGGCCAAGA +GCGGATGCAGCCCGGGATCGCCCGCACCTTCCCGTGGGCGG diff --git a/workflows/variant-calling/rna-variant-discovery/test-data/genome.gff3 b/workflows/variant-calling/rna-variant-discovery/test-data/genome.gff3 new file mode 100644 index 0000000000..eeb882669c --- /dev/null +++ b/workflows/variant-calling/rna-variant-discovery/test-data/genome.gff3 @@ -0,0 +1,43 @@ +chr22 havana pseudogene 1 2611 . + . ID=gene:ENSG00000233995;Name=AP000547.1;biotype=unprocessed_pseudogene;description=phosphoinositide-3-kinase%2C catalytic%2C alpha polypeptide (PIK3CA) pseudogene;gene_id=ENSG00000233995;logic_name=havana_homo_sapiens;version=1 +chr22 havana pseudogenic_transcript 1 2611 . + . ID=transcript:ENST00000454360;Parent=gene:ENSG00000233995;Name=AP000547.1-201;biotype=unprocessed_pseudogene;tag=basic;transcript_id=ENST00000454360;transcript_support_level=NA;version=1 +chr22 havana exon 1 124 . + . Parent=transcript:ENST00000454360;Name=ENSE00001732752;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001732752;rank=1;version=1 +chr22 havana exon 682 727 . + . Parent=transcript:ENST00000454360;Name=ENSE00001623204;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001623204;rank=2;version=1 +chr22 havana exon 1018 1186 . + . Parent=transcript:ENST00000454360;Name=ENSE00001597534;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001597534;rank=3;version=1 +chr22 havana exon 1396 1501 . + . Parent=transcript:ENST00000454360;Name=ENSE00001739921;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001739921;rank=4;version=1 +chr22 havana exon 2440 2611 . + . Parent=transcript:ENST00000454360;Name=ENSE00001596670;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001596670;rank=5;version=1 +chr22 havana exon 3337 6047 . - . Parent=transcript:ENST00000493696;Name=ENSE00003755408;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003755408;rank=3;version=1 +chr22 havana exon 8785 9261 . - . Parent=transcript:ENST00000493696;Name=ENSE00001839032;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001839032;rank=2;version=2 +chr22 havana exon 10481 10681 . - . Parent=transcript:ENST00000493696;Name=ENSE00001930505;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001930505;rank=1;version=2 +chr22 havana lnc_RNA 9051 10576 . - . ID=transcript:ENST00000472972;Parent=gene:ENSG00000239435;Name=KCNMB3P1-201;biotype=processed_transcript;transcript_id=ENST00000472972;transcript_support_level=2;version=1 +chr22 havana exon 9051 9261 . - . Parent=transcript:ENST00000472972;Name=ENSE00001878881;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001878881;rank=2;version=1 +chr22 havana exon 10481 10576 . - . Parent=transcript:ENST00000472972;Name=ENSE00001937172;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001937172;rank=1;version=1 +chr22 ensembl_havana gene 18725 20784 . - . ID=gene:ENSG00000198445;Name=CCT8L2;biotype=protein_coding;description=chaperonin containing TCP1 subunit 8 like 2 [Source:HGNC Symbol%3BAcc:HGNC:15553];gene_id=ENSG00000198445;logic_name=ensembl_havana_gene_homo_sapiens;version=4 +chr22 ensembl_havana mRNA 18725 20784 . - . ID=transcript:ENST00000359963;Parent=gene:ENSG00000198445;Name=CCT8L2-201;biotype=protein_coding;ccdsid=CCDS13738.1;tag=basic;transcript_id=ENST00000359963;transcript_support_level=NA;version=4 +chr22 ensembl_havana three_prime_UTR 18725 18850 . - . Parent=transcript:ENST00000359963 +chr22 ensembl_havana exon 18725 20784 . - . Parent=transcript:ENST00000359963;Name=ENSE00001806026;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001806026;rank=1;version=2 +chr22 ensembl_havana CDS 18851 20524 . - 0 ID=CDS:ENSP00000353048;Parent=transcript:ENST00000359963;protein_id=ENSP00000353048 +chr22 ensembl_havana five_prime_UTR 20525 20784 . - . Parent=transcript:ENST00000359963 +chr22 havana_tagene exon 20869 20949 . + . Parent=transcript:ENST00000656324;Name=ENSE00003870517;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003870517;rank=1;version=1 +chr22 havana pseudogene 23063 23459 . - . ID=gene:ENSG00000240122;Name=FABP5P11;biotype=processed_pseudogene;description=fatty acid binding protein 5 pseudogene 11 [Source:HGNC Symbol%3BAcc:HGNC:19328];gene_id=ENSG00000240122;logic_name=havana_homo_sapiens;version=1 +chr22 havana pseudogenic_transcript 23063 23459 . - . ID=transcript:ENST00000430910;Parent=gene:ENSG00000240122;Name=FABP5P11-201;biotype=processed_pseudogene;tag=basic;transcript_id=ENST00000430910;transcript_support_level=NA;version=1 +chr22 havana exon 23063 23459 . - . Parent=transcript:ENST00000430910;Name=ENSE00001596581;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001596581;rank=1;version=1 +chr22 havana_tagene exon 27394 28084 . + . Parent=transcript:ENST00000656324;Name=ENSE00003867293;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003867293;rank=2;version=1 +chr22 . biological_region 28538 28929 1 - . external_name=rank %3D 1;logic_name=firstef +chr22 . biological_region 29193 29317 1 + . external_name=rank %3D 1;logic_name=firstef +chr22 . biological_region 29193 29322 1 + . external_name=rank %3D 3;logic_name=firstef +chr22 . biological_region 29193 29381 1 + . external_name=rank %3D 4;logic_name=firstef +chr22 . biological_region 29193 30189 1 + . external_name=rank %3D 2;logic_name=firstef +chr22 havana exon 29861 30189 . + . Parent=transcript:ENST00000558085;Name=ENSE00002570186;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002570186;rank=1;version=1 +chr22 havana exon 29885 30189 . + . Parent=transcript:ENST00000400593;Name=ENSE00003795523;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003795523;rank=1;version=1 +chr22 havana exon 30018 30189 . + . Parent=transcript:ENST00000426585;Name=ENSE00001675045;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001675045;rank=1;version=1 +chr22 havana exon 29885 30189 . + . Parent=transcript:ENST00000592918;Name=ENSE00003792889;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003792889;rank=1;version=1 +chr22 havana exon 29922 30189 . + . Parent=transcript:ENST00000592107;Name=ENSE00002911043;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002911043;rank=1;version=1 +chr22 havana exon 30024 30189 . + . Parent=transcript:ENST00000591299;Name=ENSE00002800237;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002800237;rank=1;version=1 +chr22 . biological_region 29899 30635 1 - . external_name=rank %3D 1;logic_name=firstef +chr22 . biological_region 30906 30967 1 + . external_name=rank %3D 1;logic_name=firstef +chr22 . biological_region 36972 37789 1 - . external_name=rank %3D 1;logic_name=firstef +chr22 . biological_region 37540 38308 762 . . external_name=oe %3D 0.99;logic_name=cpg +chr22 havana pseudogene 3337 10681 . - . ID=gene:ENSG00000239435;Name=KCNMB3P1;biotype=transcribed_unprocessed_pseudogene;description=KCNMB3 pseudogene 1 [Source:HGNC Symbol%3BAcc:HGNC:6288];gene_id=ENSG00000239435;logic_name=havana_homo_sapiens;version=2 +chr22 havana pseudogenic_transcript 3337 10681 . - . ID=transcript:ENST00000493696;Parent=gene:ENSG00000239435;Name=KCNMB3P1-202;biotype=transcribed_unprocessed_pseudogene;tag=basic;transcript_id=ENST00000493696;transcript_support_level=NA;version=2 +chr22 havana_tagene ncRNA_gene 20869 28084 . + . ID=gene:ENSG00000287285;Name=AP000547.4;biotype=lncRNA;description=novel transcript;gene_id=ENSG00000287285;logic_name=havana_tagene_homo_sapiens;version=1 +chr22 havana_tagene lnc_RNA 20869 28084 . + . ID=transcript:ENST00000656324;Parent=gene:ENSG00000287285;Name=AP000547.4-201;biotype=lncRNA;tag=basic;transcript_id=ENST00000656324;version=1 diff --git a/workflows/variant-calling/rna-variant-discovery/test-data/mills_and_1000G.indels.vcf b/workflows/variant-calling/rna-variant-discovery/test-data/mills_and_1000G.indels.vcf new file mode 100644 index 0000000000..1063c6d69f --- /dev/null +++ b/workflows/variant-calling/rna-variant-discovery/test-data/mills_and_1000G.indels.vcf @@ -0,0 +1,63 @@ +##fileformat=VCFv4.1 +##FILTER= +##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr1.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr1.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr2.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr2.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr3.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr3.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr4.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr4.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr5.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr5.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr6.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr6.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr7.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr7.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr8.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr8.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr9.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr9.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr10.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr10.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr11.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr11.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr12.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr12.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr13.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr13.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr14.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr14.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr15.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr15.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr16.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr16.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr17.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr17.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr18.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr18.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr19.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr19.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr20.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr20.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr21.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr21.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chr22.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chr22.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/combined.phase1.chrX.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/calls/combined.phase1.chrX.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false recal_file=/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110808VQSRConsensus/VQSRData/mills100_mG8_pb0.03_QD_FS_HS_RP_IC.recal tranches_file=/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110808VQSRConsensus/VQSRData/mills100_mG8_pb0.03_QD_FS_HS_RP_IC.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub ts_filter_level=95.0 ignore_filter=null mode=INDEL" +##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[10:126450001-126600000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/chr10/AFR/AFR.phase1.chr10.844.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/chr10/ASN/ASN.phase1.chr10.844.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/chr10/AMR/AMR.phase1.chr10.844.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/chr10/EUR/EUR.phase1.chr10.844.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/chr10/AFR.admix/AFR.admix.phase1.chr10.844.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/chr10/ASN.admix/ASN.admix.phase1.chr10.844.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/chr10/AMR.admix/AMR.admix.phase1.chr10.844.raw.indels.vcf, /humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v1/calls/chr10/EUR.admix/EUR.admix.phase1.chr10.844.raw.indels.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=AFR.admix,AMR.admix,EUR.admix,ASN.admix,AFR,AMR,EUR,ASN printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 masterMerge=false mergeInfoWithMaxAC=true" +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FilterLiftedVariants="analysis_type=FilterLiftedVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/broad/shptmp/delangel/tmp/0.101786952306615.sorted.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub" +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_b36_both.fasta rodBind=[./indel_hg18_051711.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub" +##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/broad/shptmp/temporary_1000G_bams/chr1/CEU.phase1.chr1.31.cleaned.bam, /broad/shptmp/temporary_1000G_bams/chr1/FIN.phase1.chr1.31.cleaned.bam, /broad/shptmp/temporary_1000G_bams/chr1/GBR.phase1.chr1.31.cleaned.bam, /broad/shptmp/temporary_1000G_bams/chr1/IBS.phase1.chr1.31.cleaned.bam, /broad/shptmp/temporary_1000G_bams/chr1/TSI.phase1.chr1.31.cleaned.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[1:90150001-90300000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/1kg/processing/production_wgs_phase1/consensus_wgs/indel_v3/tmp/calls/chr1/alleles.chr1.602.raw.indels.vcf, /humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=50 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=GENOTYPE_GIVEN_ALLELES output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=4.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=true output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[]" +##ValidateVariants="analysis_type=ValidateVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[./indel_hg19_051711_leftAligned_collapsed.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub validationType=ALL doNotValidateFilteredRecords=false warnOnErrors=true" +##VariantAnnotator="analysis_type=VariantAnnotator input_file=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/humgen/gsa-hpprojects/dev/rpoplin/goldStandardIndel/ALL.vqsr.raw.consensus.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name= source=UNBOUND) comp=[(RodBinding name=SetBI source=/humgen/gsa-hpprojects/dev/rpoplin/goldStandardIndel/ALL.wgs.bi.20101123.leftAlignedPassingIndelsCollapsed.sites.vcf), (RodBinding name=SetDI source=/humgen/gsa-hpprojects/dev/rpoplin/goldStandardIndel/ALL.wgs.dindel.20101123.leftAlignedPassingIndels.sites.vcf), (RodBinding name=SetOX source=/humgen/gsa-hpprojects/dev/rpoplin/goldStandardIndel/ALL.wgs.oxford.20101123.leftAlignedPassingIndelsCollapsed.sites.vcf), (RodBinding name=SetSI source=/humgen/gsa-hpprojects/dev/rpoplin/goldStandardIndel/ALL.wgs.si.20101123.LeftAlignedPassingIndels.sites.vcf), (RodBinding name=SetCG source=/humgen/gsa-hpprojects/dev/rpoplin/goldStandardIndel/Complete_Public_Genomes_69genomes_all.vcf), (RodBinding name=SetML source=/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Mills_Devine_Indels_2011/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.vcf)] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub annotation=[] excludeAnnotation=[] group=[] expression=[] useAllAnnotations=false list=false vcfContainsOnlyIndels=false MendelViolationGenotypeQualityThreshold=0.0 requireStrictAlleleMatch=true filter_mismatching_base_and_quals=false" +##VariantsToVCF="analysis_type=VariantsToVCF input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_b36_both.fasta rodBind=[./indel_hg18_051711_sorted.txt] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null fixRef=true" +##contig= +##bcftools_filterVersion=1.9+htslib-1.9 +##bcftools_filterCommand=filter -r chr22:16570000-16610000 Mills_and_1000G_gold_standard.indels.hg38.chr22.vcf.gz; Date=Thu Mar 25 23:46:59 2021 +##bcftools_viewVersion=1.12+htslib-1.12 +##bcftools_viewCommand=view -O z -o mills_and_1000G.indels.rROI.vcf.gz mills_and_1000G.indels.rROI.vcf; Date=Mon Jun 14 15:21:09 2021 +##bcftools_viewCommand=view -Oz -o mills_and_1000G.indels.vcf.gz mills_and_1000G.indels.vcf; Date=Tue Jun 15 21:55:00 2021 +#CHROM POS ID REF ALT QUAL FILTER INFO +chr22 3857 . G GA 745.32 PASS set=Intersect1000GMinusSI +chr22 7065 . TTC T 423.9 PASS set=Intersect1000GAll +chr22 10413 . A AG 1291.83 PASS set=Intersect1000GAll +chr22 12195 rs3034216 C CTG 87845.9 PASS set=Intersect1000GMinusSI +chr22 12232 . AAAAG A 8475.89 PASS set=Intersect1000GMinusBI +chr22 13051 rs61605604 CT C 49330.4 PASS set=Intersect1000GMinusSI +chr22 19892 . A AT 1064.74 PASS set=Intersect1000GAll +chr22 23617 . C CT 731.83 PASS set=Intersect1000GMinusSI +chr22 29436 rs34447197 T TG 11782.8 PASS set=Intersect1000GMinusSI +chr22 34109 rs56097862 ATAGG A 3063.15 PASS set=Intersect1000GAll +chr22 35630 . A AGT 279.03 PASS set=Intersect1000GAll +chr22 39095 . G GC 462.51 PASS set=Intersect1000GAll +chr22 39277 . AAAAAG A 581.13 PASS set=Intersect1000GMinusSI +chr22 39780 . CG C 1261.91 PASS set=Intersect1000GAll diff --git a/workflows/variant-calling/rna-variant-discovery/test-data/test_rnaseq_1.fastq.gz b/workflows/variant-calling/rna-variant-discovery/test-data/test_rnaseq_1.fastq.gz new file mode 100644 index 0000000000..bf873e51b6 Binary files /dev/null and b/workflows/variant-calling/rna-variant-discovery/test-data/test_rnaseq_1.fastq.gz differ diff --git a/workflows/variant-calling/rna-variant-discovery/test-data/test_rnaseq_2.fastq.gz b/workflows/variant-calling/rna-variant-discovery/test-data/test_rnaseq_2.fastq.gz new file mode 100644 index 0000000000..5a96ec4619 Binary files /dev/null and b/workflows/variant-calling/rna-variant-discovery/test-data/test_rnaseq_2.fastq.gz differ