if ( ! passesCallThreshold(phredScaledConfidence) )
builder.filter(LOW_QUAL_FILTER_NAME);
// create the genotypes
final GenotypesContext genotypes = afCalculator.subsetAlleles(vc, defaultPloidy, outputAlleles, true);
builder.genotypes(genotypes);
// *** note that calculating strand bias involves overwriting data structures, so we do that last
final Map<String, Object> attributes = composeCallAttributes(inheritAttributesFromInputVC, vc, rawContext, stratifiedContexts, tracker, refContext,
outputAlternativeAlleles.alternativeAlleleMLECounts(), outputAlternativeAlleles.siteIsMonomorphic, AFresult, outputAlternativeAlleles.outputAlleles(vc.getReference()),genotypes,model,perReadAlleleLikelihoodMap);