VariantEval/GenotypeConcordance stratify by depth-of-coverage, genotype quality, or other metric?
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I would like to evaluate variant calls to produce a plot (psuedo-ROC) of sensitivity vs. specificity (or concordance, etc) when I condition on a minimum/maximum value for a particular metric (coverage, genotype quality, etc.). I can do this by running VariantEval or GenotypeConcordance multiple times, once for each cutoff value, but this is inefficient, since I believe I should be able to compute these values in one pass. Alternatively, if there was a simple tool to annotate each variant as concordance or discordant, I could tabulate the results myself. I would like to rely upon GATK's variant comparison logic to compare variants (especially indels). Any thoughts on if current tools can be parameterized, or adapted for these purposes?

Thanks for your help in advance,

N


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