Issue with getting all indels being incorporated

[juanfmacias3]

So I am trying to figure out how to use this program and I decided to make some fake data to test it all out. I created a fake genome and some VCF files to along with it.

Indels:

SNPS:

fakeGenome:

I run the program like so:

build_new_sequence_from_vcfs.py -r fakeGenome.fa -s SNPS.vcf -i Indels.vcf -o replaced.fa LG

It appears to make most of the changes, but does not make the last indel change.

Am I missing anything simple? Is it because it is near the end of the sequence?

[AlSimonsJax]

Hi,

I'll take a look at this, but it probably won't be until mid-next week. I'd appreciate it if you would send the actual files to al.simons@jax.org.
Thanks!
-Al

From: juanfmacias3 <notifications@github.commailto:notifications@github.com>
Reply-To: jaxcs/Seqnature <reply@reply.github.commailto:reply@reply.github.com>
Date: Thursday, August 11, 2016 at 1:02 PM
To: jaxcs/Seqnature <Seqnature@noreply.github.commailto:Seqnature@noreply.github.com>
Subject: [jaxcs/Seqnature] Issue with getting all indels being incorporated (#4)

So I am trying to figure out how to use this program and I decided to make some fake data to test it all out. I created a fake genome and some VCF files to along with it.

Indels:
[Indels]https://cloud.githubusercontent.com/assets/2448982/17597276/a4036690-5fba-11e6-9bc3-bb7fece90f83.png

SNPS:
[SNPs]https://cloud.githubusercontent.com/assets/2448982/17597307/c62823f0-5fba-11e6-9670-aec6c7782e6b.png

fakeGenome:
[Genome]https://cloud.githubusercontent.com/assets/2448982/17597326/dfa5c3e6-5fba-11e6-88db-95710d50c86d.png

I run the program like so:

build_new_sequence_from_vcfs.py -r fakeGenome.fa -s SNPS.vcf -i Indels.vcf -o replaced.fa LG

It appears to make most of the changes, but does not make the last indel change.

[alignment]https://cloud.githubusercontent.com/assets/2448982/17597426/532e3abe-5fbb-11e6-8926-8a181cd1d515.png

Am I missing anything simple? Is it because it is near the end of the sequence?

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