Description

Finds mendelian violations of all types within a VCF. Takes in VCF or BCF and a pedigree file and looks for high confidence calls where the genotype of the offspring is incompatible with the genotypes of the parents. Assumes the existence of format fields AD, DP, GT, GQ, and PL fields. Take note that the implementation assumes that reads from the PAR will be mapped to the female chromosome rather than the male. This requires that the PAR in the male chromosome be masked so that the aligner has a single coting to map to. This is normally done for the public releases of the human reference.