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