Does the relationship between AD and DP stil hold in VCF produced from ReduceRead BAMs?
That is the sum of AD is <= DP
Or can other scenarios now occur?
Also is AD summarized to 1,0 or 0,1 for homozygous REF and ALT?
Unfortunately I literally -- like 2 minutes ago -- fixed a bug where the DP for indels wasn't being calculated correctly. Going forward the AD <= DP should hold for reduced reads but if you are looking at indels right now I'd take DP ~= sum(AD)
Everything should be fine for snps. And no, it's full read depth counts, so you see lines like 50,0:55 for AD and DP even from reduced reads output.
No, Monkol is correct. My fixes for annotations (DP, AD, and FS) won't make it public until the upcoming 2.2 release.
But it should be okay for SNPs?
Also does ReduceRead cause the AD to be summarized to 1,0 or 0,1 for homozygotes?