If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
What is PL 0,0?
I have a genomics data from Bacteria (E. Coli.) and used GATK 4 for variant calling. I have noticed that for some samples and some loci, PL is 0,0. Can anyone please explain this?
eg. NC_000913 4473651 . C . . . GT:AD:DP:GQ:PL 0:2,0:2:0:0,0
How can we interpret that? becuase in this case, the GT in later steps will be "." as it will be driven from PL, when we combine and genotype the samples.
thanks in advance.