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.
getting high quality monomorphic sites from GenotypeGVCFs
I am doing a population genetic analysis and am consequently very interested in obtaining high confidence monomorphic sites.
I used GATK 3.1 HaplotypeCaller in the new incremental variant discovery pipeline and then ran GenotypeGVCFs using the -inv option so as to print non variant sites after combining.
A monomorphic record looks like this:
scaffold_1 202986 . G . . . . GT:AD:DP:PL ./.:81:81:0 ./.:6:12:0 ./.:0:0:0 .....etc
I had a couple of questions:
It seems GT, GQ, and PL is no longer reported after combining for monomorphic sites? is there a reason why? I'm asking because I'd like to be able to distinguish high qual (first genotype) / low qual (second genotype) monomorphic sites so I can change the low qual sites to missing (third genotype).
If getting high confidence monomorphic sites is my goal, would you recommend that I do my own parsing starting with the individual gvcfs rather than using the GenotypeGVCFs walker?
thanks much for your help!
Young Wha Lee