If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
I am using GATK version 3.3 (latest release) and following the best practice for variant calling. Steps i am using is
1. Run haplotye caller and get the gVCF file
2. Run GenotypeGVCF across the samples to the get the VCF file
The Question is about the Genotype calling.
Here is an example:
GVCF file looks like this for a particular position
chr1 14677 . G . . END=14677 GT:DP:GQ:MIN_DP:PL 0/0:9:0:9:0,0,203
VCF file looks like this after genotyping with multiple samples.
chr1 14677 . G A 76.56 PASS . . GT:AD:DP:GQ:PL 0/1:8,1:9:4:4,0,180
In GVCF file there was no support for the alternate allele, but VCF file shows that there are 1 read supporting the alternate call.
Thanks ! Saurabh