Haplotype-based variant detection from short-read sequencing

Erik Garrison, Gabor Marth
7/17/2012
q-bio.GNq-bio.QM

Official code: freebayes/freebayes (880 stars, MIT, last commit 2026-09-03).

Abstract

The direct detection of haplotypes from short-read DNA sequencing data requires changes to existing small-variant detection methods. Here, we develop a Bayesian statistical framework which is capable of modeling multiallelic loci in sets of individuals with non-uniform copy number. We then describe our implementation of this framework in a haplotype-based variant detector, FreeBayes.

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Code Implementations(1)

freebayes/freebayesOfficial100%
MIT

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

880275C, ROct 13, 20101 months agoMIT

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Cite this paper

@article{garrison2012haplotypebased,
  title  = {Haplotype-based variant detection from short-read sequencing},
  author = {Erik Garrison and Gabor Marth},
  year   = {2012},
  eprint = {1207.3907},
  archivePrefix = {arXiv},
  url    = {https://arxiv.org/abs/1207.3907}
}

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