Issues

• Resource allocation tweaks

  uclahs-cds/pipeline-call-gSNP#194 · Filter by author yashpatel6 opened on Mar 26, 2025
  

• Use store_object_as_json to store parameters

  standardization
  uclahs-cds/pipeline-call-gSNP#180 · Filter by author nwiltsie opened on Aug 12, 2024

• GATK Trio mode best-practices

  uclahs-cds/pipeline-call-gSNP#178 · Filter by author yashpatel6 opened on Aug 3, 2024
  

• GATK v4.6.2.0

  uclahs-cds/pipeline-call-gSNP#176 · Filter by author yashpatel6 opened on Jul 1, 2024
  

• Use methods.setup_process_afterscript() for process logs

  uclahs-cds/pipeline-call-gSNP#172 · Filter by author nwiltsie opened on Jun 10, 2024
  

• docker-gatk name update

  uclahs-cds/pipeline-call-gSNP#164 · Filter by author yashpatel6 opened on May 7, 2024

• GATK v3.7.0 Docker image update name

  uclahs-cds/pipeline-call-gSNP#163 · Filter by author yashpatel6 opened on May 7, 2024

• Update VQSR commands to follow recent GATK best practices

  uclahs-cds/pipeline-call-gSNP#133 · Filter by author tnyamaguchi opened on Jun 1, 2023

• Compress raw VCFs

  uclahs-cds/pipeline-call-gSNP#124 · Filter by author yashpatel6 opened on Feb 25, 2023

• Contamination file extension

  uclahs-cds/pipeline-call-gSNP#117 · Filter by author yashpatel6 opened on Dec 20, 2022

• Error: Invalid parameter type for parameter input_csv

  uclahs-cds/pipeline-call-gSNP#111 · Filter by author alkaZeltser opened on Nov 5, 2022
  1

• Process multi_sample_wgs:recalibrate_base:run_ApplyBQSR_GATK (30) terminated with an error exit status (3)

  uclahs-cds/pipeline-call-gSNP#103 · Filter by author graceooh opened on Aug 25, 2022
  2

  

• Move dev test files - call-gSNP - @yashpatel6

  uclahs-cds/pipeline-call-gSNP#98 · Filter by author yashpatel6 opened on Jul 13, 2022
  

• scatter_count > 50

  uclahs-cds/pipeline-call-gSNP#73 · Filter by author RoniHaas opened on Mar 19, 2022
  5

• Update VCF filtration and QC

  uclahs-cds/pipeline-call-gSNP#68 · Filter by author yashpatel6 opened on Mar 9, 2022
  

• Review the Perl filtering script

  enhancement
  uclahs-cds/pipeline-call-gSNP#67 · Filter by author yashpatel6 opened on Mar 5, 2022
  

• Registered dataset input/methods

  uclahs-cds/pipeline-call-gSNP#59 · Filter by author yashpatel6 opened on Feb 4, 2022
  

• Error paired_sample_wgs:reheader_interval_bams

  uclahs-cds/pipeline-call-gSNP#50 · Filter by author tgebo opened on Jan 5, 2022
  2

  

• Errorpaired_sample_wgs:remove_realigned_bams

  uclahs-cds/pipeline-call-gSNP#49 · Filter by author tgebo opened on Jan 5, 2022

• Use singleID instead of normalID when there is only one sample from a patient

  enhancement
  uclahs-cds/pipeline-call-gSNP#17 · Filter by author shutaojccc opened on Sep 1, 2021
  1

• Update Dockerfile for SNV filtering script

  uclahs-cds/pipeline-call-gSNP#8 · Filter by author yashpatel6 opened on Aug 13, 2021