I performed a variant caller comparison, and the genotype concordance analysis of HaplotypeCaller's results a little strange to me, and I can't understand it at all.
ALLELES_MATCH: 0 EVAL_SUPERSET_TRUTH: 2438 EVAL_SUBSET_TRUTH: 0 ALLELES_DO_NOT_MATCH: 636 EVAL_ONLY: 20 TRUTH_ONLY: 1014546
The last and first value could be true? Or anyone can tell what could cause this? I got very different (and reasonable) results e.g. with samtools.