Overview
freebayes is a Bayesian genetic variant detector designed to identify small polymorphisms, including SNPs, indels, MNPs, and complex events, using short-read sequencing data. It uses a haplotype-based approach, calling variants based on the literal sequences of reads aligned to a target, rather than precise alignment. This addresses the issue of multiple possible alignments for identical sequences. The tool takes BAM files (Phred+33 encoded quality scores) from multiple individuals and a FASTA reference genome to determine the most probable combination of genotypes at each reference position, outputting polymorphic positions in VCF format. It can utilize prior information from input VCF files and copy number variant maps (BED) to account for non-uniform ploidy variation. Freebayes is parallelizable using the freebayes-parallel wrapper, leveraging GNU parallel to process different genomic regions concurrently.
Common tasks