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.
A preprint Haplotype-based variant detection from short-read sequencing provides an overview of the statistical models used in FreeBayes. We ask that you cite this paper if you use FreeBayes in work that leads to publication.
Please use this citation format:
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012
If possible, please also refer to the version number provided by freebayes when it is run without arguments or with the –help option. For example, you should see something like this:
version: v0.9.10-3-g47a713e-dirty