Haplotype-based variant detection from short-read sequencing
Erik Garrison, Gabor Marth
(Submitted on 17 Jul 2012 (v1), last revised 20 Jul 2012 (this version, v2))

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.