nickzren / atav Goto Github PK

I see in the user guide a reference to an atav.sh file, however, this does not appear to exist in this repo. How do users interact with the cli? Is there some installation process?

Hi Nick,

In looking at output from --list-vcf, I noticed that ATAV will report homozygous reference for genotypes. In the original ticket to design the feature, you wrote the following...

Genotype: Hom --> 1/1 Het --> 1/0 Hom Ref --> 0/0 NA --> ./.

I'm curious about Hom Ref. I though ATAV didn't store reference genotypes. When we do collapsing, we assume hom ref if DP > 10 but no variant. Is this the same? Or is ATAV actually storing hom ref for some sites? Also, in what circumstances would ATAV store NA? Does that mean there is dp < 10 for that site?

Thanks!