freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping

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Bayesian haplotype-based genetic polymorphism discovery and genotyping

freebayes

Call variants from a BAM file against a reference genome$ freebayes -f reference.fasta input.bam > output.vcf

Call variants with specified region and minimum coverage$ freebayes -f reference.fasta -r chr1:1000-2000 -m 20 input.bam > output.vcf

Call variants from multiple BAM files with ploidy setting$ freebayes -f reference.fasta -p 2 sample1.bam sample2.bam > output.vcf