title: pyGenClean: efficient tool for genetic data clean up before association testing.
abstract: Genetic association studies making use of high-throughput genotyping arrays need to process large amounts of data in the order of millions of markers per experiment. The first step of any analysis with genotyping arrays is typically the conduct of a thorough data clean up and quality control to remove poor quality genotypes and generate metrics to inform and select individuals for downstream statistical analysis. We have developed pyGenClean, a bioinformatics tool to facilitate and standardize the genetic data clean up pipeline with genotyping array data. In conjunction with a source batch-queuing system, the tool minimizes data manipulation errors, accelerates the completion of the data clean up process and provides informative plots and metrics to guide decision making for statistical analysis.
  
  
  METHODS
  pyGenClean is an open source Python 2.7 software and is freely available, along with documentation and examples, from http://www.statgen.org.
authors: Montreal Heart Institute Research Center, Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, 5000 Bélanger Street, Montréal, Canada. louis-philippe.lemieux.perreault@umontreal.ca
authors: Louis-Philippe
authors: LP
authors: Lemieux Perreault
authors: Sylvie
authors: S
authors: Provost
authors: Marc-André
authors: MA
authors: Legault
authors: Amina
authors: A
authors: Barhdadi
authors: Marie-Pierre
authors: MP
authors: Dubé
mesh_terms: D056726:Genetic Association Studies; D060005:Genotyping Techniques / Q000592:standards*; D006801:Humans; D011786:Quality Control; D012984:Software
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