IBDseq

IBDseq is a method for detecting identity by descent (IBD) segments in sequence data, along with a method called SEQERR for estimating genotype error rates at low-frequency variants using detected IBD. The IBDseq method estimates probabilities of genotypes observed with error for each pair of individuals under IBD and non-IBD models, achieving high power and accuracy for IBD detection in sequence data. SEQERR estimates genotype error rates by comparing observed and expected rates of pairs of homozygote and heterozygote genotypes at low-frequency variants in IBD segments. The software is evaluated under multiple parameter settings and is shown to be accurate in simulated data and real-world data from the UK10K and 1000 Genomes projects.

Topic

Mapping

Detail

  • Operation: Sequence analysis;Genetic mapping

  • Software interface: Command-line user interface

  • Language: Java

  • License: Apache-2.0, MIT License

  • Cost: Free

  • Version name: r1206

  • Credit: This study makes use of data generated by the Wellcome Trust Case-Control Consortium. A full list of the WTCCC investigators who contributed to the generation of the data is available online. Funding for the project was provided by the Wellcome Trust under awards 076113 and 085475. This study makes use of data generated by the UK10K Consortium, derived from samples from UK10K_COHORTS_TWINSUK and UK10K_COHORT_ALSPAC cohorts. A full list of the UK10K investigators who contributed to the generation of the data is available online. Funding for UK10K was provided by the Wellcome Trust under award WT091310. This study was supported by research grants HG004960, HG005701, GM075091 from the National Institutes of Health, USA.

  • Input: -

  • Output: -

  • Contact: browning@uw.edu

  • Collection: -

  • Maturity: -

Publications

  • Detecting identity by descent and estimating genotype error rates in sequence data.
  • Browning BL and Browning SR. Detecting identity by descent and estimating genotype error rates in sequence data. Detecting identity by descent and estimating genotype error rates in sequence data. 2013; 93:840-51. doi: 10.1016/j.ajhg.2013.09.014
  • https://doi.org/10.1016/j.ajhg.2013.09.014
  • PMID: 24207118
  • PMC: PMC3824133

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