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freebayes

Bayesian variant caller for detecting genetic polymorphisms in DNA sequences.

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About

Bayesian haplotype-based genetic polymorphism discovery and genotyping

Commands

freebayes

Examples

call variants from a BAM file against a reference genome$ freebayes -f reference.fasta sample.bam > variants.vcf
genotype multiple samples together in parallel$ freebayes -f reference.fasta -L samples.txt --region chr1:1000-2000 > region.vcf
call variants with minimum coverage threshold$ freebayes -f reference.fasta --min-coverage 10 sample.bam > filtered_variants.vcf
detect SNPs and indels across a specific genomic region$ freebayes -f reference.fasta --region chr1:100000-200000 sample.bam > region_variants.vcf
call variants with custom allele frequency and quality filters$ freebayes -f reference.fasta --min-alternate-fraction 0.05 -q 20 sample.bam > variants.vcf