GENOTYPECHECKER: an interactive tool for checking the inheritance consistency of genotyped pedigrees

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Abstract

Datapoint errors in pedigree genotype data sets are difficult to identify and adversely affect downstream genetic analyses. We present GENOTYPECHECKER, a desktop software tool for assisting data cleansing. The application identifies likely data errors in pedigree/genotype data sets by performing an inheritance-checking algorithm for each marker across the pedigree, and highlights inconsistently inherited genotypes in an exploratory user interface. By 'masking' suspect datapoints and rechecking inheritance consistency, erroneous datapoints can be confirmed and cleansed from the data set. The software, examples and documentation are freely available at http://bioinformatics.roslin.ac.uk/genotypechecker.
Original languageEnglish
Pages (from-to)560-562
Number of pages3
JournalAnimal Genetics
Volume42
Issue number5
DOIs
Publication statusPublished - Oct 2011

Keywords

  • data cleaning genome analysis genotyping linkage analysis population genetics

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