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.

reference sites FORMAT output

Is it possible to report GT:AD:DP:GQ:PL for sites with reference calls just like the sites with snp/indel calls? In the example below, I have a position with reference call and a position wiht indel.
chr1 11863158 . T . . . DP=1994;MQ=48.86;MQ0=90 GT ./.
chr1 16055173 . AGA A 0 LowQual AC=0;AF=0.00;AN=2;DP=92;ExcessHet=3.0103;FS=0.000;MLEAC=0;MLEAF=0.00;MQ=49.45;MQ0=0;SOR=0.011 GT:AD:DP:GQ:PL 0/0:50,0:90:99:0,150,2034

Best Answer


Sign In or Register to comment.