Haplotype-based variant detection from short-read sequencing
  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. 
Erik Garrison and Gabor Marth
q-bio.GN q-bio.QM