return vc.getGenotypes();
final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
for ( final Genotype genotype : vc.getGenotypes() ) {
AlignmentContext context = null;
PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = null;
if (stratifiedContexts != null)
context = stratifiedContexts.get(genotype.getSampleName());
if (stratifiedPerReadAlleleLikelihoodMap != null)
perReadAlleleLikelihoodMap = stratifiedPerReadAlleleLikelihoodMap.get(genotype.getSampleName());