Freebayes

Bayesian haplotype-based polymorphism discovery and genotyping

FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs single-nucleotide polymorphisms, indels insertions and deletions, MNPs multi-nucleotide polymorphisms, and complex events composite insertion and substitution events smaller than the length of a short-read sequencing alignment.

WWW https//github.com/ekg/freebayes