Stratify comp rods by sample in VariantEval?
Posted in Ask the GATK team | Last updated on


Comments (3)

Hi GATK Team,

I am heavy user of the VariantEval evaluators (particularly GenotypeConcordance) and tracked some unexpected results to the Sample stratification. What is the motivation for not stratifying the comp RODs by the sample? This seems to be a very conscious choice so I was hoping to understand the background of that choice

The relevant section of VariantEval.java is:

for ( final RodBinding<VariantContext> compRod : comps ) {
                            // no sample stratification for comps
                            final HashMap<String, Collection<VariantContext>> compSetHash = compVCs.get(compRod);
                            final Collection<VariantContext> compSet = (compSetHash == null || compSetHash.size() == 0) ? Collections.<VariantContext>emptyList() : compVCs.get(compRod).values().iterator().next();

The effect for me is that many spurious genotypes get included in cases where is a comp variant, but not eval variant.

Thanks!


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