Roslin Bioinformatics - Genotype Checker
A Desktop Application for Checking the Inheritance Consistency of Pedigree/Genotype Data
Roslin's ResSpecies GenotypeChecker is a desktop tool for identifying likely data errors in pedigree/genotype datasets and to assist data cleansing.
Datapoint errors in pedigree genotype datasets are difficult to identify and adversely affect downstream genetic analyses. Errors that are inconsistent with the rules of Mendelian inheritance typically invalidate linkage analysis algorithms, and cause such analyses to fail. Genotype errors may arise from a variety of systematic or sporadic errors in either the genotyping assay, or in recording the pedigree or genotype information.
By applying an inheritance-checking algorithm for markers across the pedigree and visualising the inheritance data in an exploratory user interface, GenotypeChecker allows the sources of data inconsistency can be resolved.
GenotypeChecker displays the marker genotypes for individuals in the pedigree in tabular form (individual versus marker). Applying the inheritance-checking algorithm across the pedigree for each marker both infers missing genotype data and highlights genotypes that are not consistent with the basic rule that an offspring's genotype must derive from alleles inherited from each parent.
The manner in which the algorithm traverses the pedigree data means that the exact position that an error is reported can vary, i.e. an error reported in an individual genotype may actually be because there is an actual error in a near relative e.g. a parent. In practice the error reporting is pushed down the generations, so an error reported in generation 4 might be due to a mistyping or misrecording of a genotype in a preceding generation.