FreeBayes

     

--------

Note that CI tests may fail until vcflib is updated on the main distros to 1.0.13. This is because of the location of vcflib include files moved to /usr/include/vcflib.

*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.

freebayes is haplotype-based, in the sense that it calls variants based on

the literal sequences of reads aligned to a particular target, not their

precise alignment. This model is a straightforward generalization of previous

ones (e.g. PolyBayes, samtools, GATK) which detect or report variants based on

alignments. This method avoids one of the core problems with alignment-based

variant detection--- that identical sequences may have multiple possible

alignments:

<img src="https://github.com/freebayes/freebayes/raw/v1.3.0/paper/haplotype_calling.png" width=500/>

freebayes uses short-read alignments

(BAM files with

Phred+33 encoded quality

scores, now standard) for any number of individuals from a population and a

reference genome (in

FASTA format)

to determine the most-likely combination of genotypes for the population at

each position in the reference. It reports positions which it finds putatively

polymorphic in variant call file (VCF)

format. It can also use an input set of variants (VCF) as a source of prior

information, and a copy number variant map (BED) to define non-uniform ploidy

variation across the samples under analysis.

freebayes is maintained by Erik Garrison and Pjotr Prins. See also [RELEASE-NOTES](./RELEASE-NOTES.md).

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.

This preprint is used for documentation and citation.

freebayes was never submitted for review, but has been used in over 1000 publications.

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.

freebayes is provided as a pre-built 64-bit static Linux binary as part of releases.

Debian and Conda packages should work too, see the badges at the top

of this page.

To build freebayes from source check the

[development](#Development) section below. It is important to get the full recursive

git checkout and dependencies.

Please report any issues or questions to the freebayes mailing list. Report bugs on the freebayes issue tracker