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.
Reading haplotype caller
6 31324601 rs9281379 C CA,CG 158601.1 . AC=1,1;AF=0.500,0.500;AN=2;DB;DP=3697;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.26;QD=29.97;SOR=0.751 GT:AD:DP:GQ:PL 1/2:0,1756,1926:3682:99:158618,52177,41139,71967,0,65397
With respect to the output of haplotype caller, can you please explain what does "1/2" mean in genotype?
Is it that the reference allele is not present in the sequence and one strand has CA and other has CG?