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.
SNP genotyping problem, along with AD, DP
I used an older version of GATK and did a SNP calling from Haplotype caller (HaplotypeCaller,Version=2.7-2-g6bda569). Now I went back to the vcf file, but noticed some genotyping that I don't understand:0/1:0,13:13:PASS:99:457,0,543, where does the "0/1" come from?