GENCHECK: A program for consistency checking and derivation of genotypes at co-dominant and dominant loci

The program GENCHECK was developed to examine genotyping results of diploid organisms for consistency with the Mendelian laws of inheritance. It can be used to analyse data from co-dominant and dominant loci and large scale pedigrees with many overlapping generations as they are common in animal breeding. The pedigree data and genotyping results are read either from a suitable database or from an ASCII file. The data from individuals, whose genotyping results show a Mendelian segregation error, are written to an output file. Possible error sources can be a result from genotyping errors, false parentage and erroneous data transfer. Additionally, the program derives, if possible, the genotypes of untyped individuals or of individuals, whose genotyping results were assumed to cause a Mendelian segregation error, using information from the parents and/or the offspring. Error checking and derivation of genotypes are combined in a single computation step. Important technical solutions for example, the examination of genotyping results from dominant loci, the representation of possible genotypes on the bit-level and the dependency of the results on ordering individuals in different ways are discussed. The program is written in Fortran 90 and available from the authors.