<commit_before># *freebayes*, a haplotype-based variant detector
## user manual and guide

### <NAME> <<EMAIL>>

--------

## Overview

[*FreeBayes*](http://arxiv.org/abs/1207.3907) is a 
[Bayesian](http://en.wikipedia.org/wiki/Bayesian_inference) 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="http://hypervolu.me/freebayes/figures/haplotype_calling.png" 
width=500/>

*FreeBayes* uses short-read alignments 
([BAM](http://samtools.sourceforge.net/SAMv1.pdf) files with 
[Phred+33](http://en.wikipedia.org/wiki/Phred_quality_score) encoded quality 
scores, now standard) for any number of individuals from a population and a 
[reference genome](http://en.wikipedia.org/wiki/Reference_genome) (in 
[FASTA](http://en.wikipedia.org/wiki/FASTA_format) 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](http://www.1000genomes.org/node/101)) 
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.


## Citing freebayes

A preprint [Haplotype-based variant detection from short-read 
sequencing](http://arxiv.org/abs/1207.3907) 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.

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

This provides both a point release number and a git commit id, which will 
ensure precise reproduction of results.


## Obtaining

To download FreeBayes, please use git to download the most recent development
tree.  Currently, the tree is hosted on github, and can be obtained via:<commit_msg>reminder to cite freebayes using DOI rather than URL<commit_after># *freebayes*, a haplotype-based variant detector
## user manual and guide

### <NAME> <<EMAIL>>

--------

## Overview

[*FreeBayes*](http://arxiv.org/abs/1207.3907) is a 
[Bayesian](http://en.wikipedia.org/wiki/Bayesian_inference) 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="http://hypervolu.me/freebayes/figures/haplotype_calling.png" 
width=500/>

*FreeBayes* uses short-read alignments 
([BAM](http://samtools.sourceforge.net/SAMv1.pdf) files with 
[Phred+33](http://en.wikipedia.org/wiki/Phred_quality_score) encoded quality 
scores, now standard) for any number of individuals from a population and a 
[reference genome](http://en.wikipedia.org/wiki/Reference_genome) (in 
[FASTA](http://en.wikipedia.org/wiki/FASTA_format) 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](http://www.1000genomes.org/node/101)) 
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.


## Citing freebayes

A preprint [Haplotype-based variant detection from short-read 
sequencing](http://arxiv.org/abs/1207.3907) 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:

    <NAME>, <NAME>. 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

This provides both a point release number and a git commit id, which will 
ensure precise reproducibility of results.


## Obtaining

To download FreeBayes, please use git to download the most recent development
tree.  Currently, the tree is hosted on github, and can be obtained via:
{'fraction_non_alphanumeric': 0.07892906815020863, 'fraction_numerical': 0.01564673157162726, 'mean_word_length': 4.640196078431373, 'pattern_counts': {'":': 0, '<': 13, '<?xml version=': 0, '>': 13, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6281570', 'n_tokens_mistral': 1777, 'n_tokens_neox': 1586, 'n_words': 683}