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.
I got the information in my VCF file like this
4 41748013 . CGCCGCCGCTGCCGCG *,C 6095.25 PASS AC=9,22;AN=1266 GT:AD:DP:GQ:PGT:PID:PL 0/0:3,0,0:3:6:.:.:0,6,90,6,90,90 0/0:4,0,0:4:12:.:.:0,12,132,12,132,132
Many samples have very low DP even one read but this variant is annotated with PASS.
I am wondering is it a false positive in calling? Can I believe this or not?