Freebayes
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Application data |
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| Created by | Erik Garrison |
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| Biological application domain(s) | Genomics |
| Created at | Boston College |
| Maintained? | Yes |
| Input format(s) | BAM |
| Output format(s) | VCF |
| Licence | MIT |
Summary: Bayesian genetic variant detector (SNPs, indels, MNPs)
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Contents
Description
FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), and MNPs (multi-nucleotide polymorphisms) smaller than the length of a short-read sequencing alignment. It uses short-read alignments (BAM files with Phred+33 encoded quality scores) for any number of individuals from a population and a reference genome to determine the most-likely combination of genotypes for the population at each position in a reference genome (FASTA). It reports positions which it finds to be more likely polymorphic than monomorphic in a standard variant interchange format (VCF).
Manual seems to indicate that Freebayes will work with both indexed (barcoded, or separately run samples so that individual is known for each read) or non-indexed pooled reads.
Usage
In its simplest form (finding SNPs versus a reference) Freebayes can be run by just typing :
./freebayes --fasta-reference input.fa aligned.bam.
Links
References
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