How does PBAT handle Mendelian errors?

On a SNP by SNP basis, Mendelian errors are evaluated for each family. If there is a Mendelian error in that family, all genotypes on all family members for that SNP will be removed. 

Note that PBAT does this "under the hood" and doesn't give the explicit results. We recommend first running the data through a pedigree checking program as well as a genotype checking program ( e.g. pedcheck).