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Identification of Genotype Errors

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Statistical Human Genetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 850))

Abstract

It has been documented that there exist some errors in most large genotype datasets and that an error rate of 1–2% is adequate to lead to the distortion of map distance as well as a false conclusion of linkage (Abecasis et al. Eur J Hum Genet 9(2):130–134, 2001), therefore one needs to ensure that the data are as clean as possible. On the other hand, the process of data cleaning is tedious and demands efforts and experience. O’Connell and Weeks implemented four error-checking algorithms in computer software called PedCheck. In this chapter, the four algorithms implemented in PedCheck are discussed with a focus on the genotype-elimination method. Furthermore, an example for four levels of error checking permitted by PedCheck is provided with the required input files. In addition, alternative algorithms implemented in other statistical computing programs are also briefly discussed.

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Acknowledgments

The views expressed in this chapter do not necessarily represent the views of the NIMH, NIH, HHS, or the US Government.

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Authors and Affiliations

  1. Unit of Statistical Genomics, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA

    Yin Y. Shugart

  2. Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Ying Wang

Authors
  1. Yin Y. Shugart
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  2. Ying Wang
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Corresponding author

Correspondence to Yin Y. Shugart .

Editor information

Editors and Affiliations

  1. School of Medicine, Dept. Epidemiology & Biostatistics, Case Western Reserve University, Cornell Road 2103, Cleveland, 44106, Ohio, USA

    Robert C. Elston

  2. Dept. Epidemiology & Biostatistics, Memorial Sloan-Kettering Cancer Center, East 63rd Street 307, New York, 10021, New York, USA

    Jaya M. Satagopan

  3. School of Medicine, Dept. Epidemiology & Biostatistics, Case Western Reserve University, Cornell Road 2103, Cleveland, 44106, Ohio, USA

    Shuying Sun

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Shugart, Y.Y., Wang, Y. (2012). Identification of Genotype Errors. In: Elston, R., Satagopan, J., Sun, S. (eds) Statistical Human Genetics. Methods in Molecular Biology, vol 850. Humana Press. https://doi.org/10.1007/978-1-61779-555-8_2

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  • DOI: https://doi.org/10.1007/978-1-61779-555-8_2

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-554-1

  • Online ISBN: 978-1-61779-555-8

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