the --genome --rel-check options in PLINK. Using HapMap trio samples it is also possible to inspect each SNP for Mendelian inconsistencies, which indicate genotyping errors if pedigree information is correct. Mendelian inconsistencies can be assessed using the --mendel option in PLINK. PLINK only detects Mendelian inconsistencies in full trios. The Mendelian-error procedure in PLATO will also evaluate Mendelian consistency in parent-offspring pairs or sib-pairs with missing parental genotypes.
