vcfeval --roc-subset behavior

[Glenn Carson]

It looks like --roc-subset supports multiple variant types to be provided, e.g. --roc-subset hom,snp. However, so far it seems like the tool treats those as multiple separate restrictions (roc file for SNP's, and another for homozygous variants) rather than a unified restriction (roc file for homozygous SNP's). 

I wanted to sanity check if anyone was aware of a way to restrict in this way (dual restriction for SNP's that are homozygous). I wonder if --roc-expr would be a good way to do this. I could look for homozygous calls (GT: 1|1, 0|0) and restrict to single nucletide ALT's. 

Any ideas?

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[Len Trigg]

Hi Glenn,

Yes, you should be able to use --roc-expr to do what you want.

It also turns out that we have a contributed PR that would probably achieve what you want -- essentially a flag that allows interpreting multiple roc subsets as outputting a cross product of their conditions (so if you gave --roc-subset het,hom,snp you would end up with two output roc files, one for het snps, and one for hom snps). If you're technically minded you could build that and have a play (https://github.com/RealTimeGenomics/rtg-tools/pull/13).

Cheers,

Len.

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