Meaning of terms in output of GenotypeConcordance
Just to make sure my understanding is correct:
HET: heterozygous HOM_REF: homozygous reference HOM_VAR: homozygous variant MIXED: something like `./1` Mismatching_Alleles: ?? UNAVAILABLE: for internal use ALLELES_MATCH: ?? ALLELES_DO_NOT_MATCH: ?? EVAL_ONLY: ?? TRUTH_ONLY: does it actually mean the variants present in comp but not in eval, like COMP_ONLY?
how does the following computed?
Non-Reference_Discrepancy Non-Reference_Sensitivity Overall_Genotype_Concordance
Thanks a lot!