README.md

bcftools container

Main tool:

• https://www.htslib.org/
• GitHub

Additional tools:

• perl 5.30.0

Example Usage

bcftools mpileup -A -d 200 -B -Q 0 -f {reference_genome} {bam} | bcftools call -mv -Ov -o bcftools_variants/{sample}.vcf

Better documentation can be found at https://www.htslib.org/doc/bcftools.html