Main tool: bcftools
Code repository: https://github.com/samtools/bcftools
Basic information on how to use this tool:
- executable:
bcftools - help:
--help - version:
--version - description: BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.
Additional information:
This container includes bcftools compiled with libdeflate for a better cloud performance. Also, "polysomy" and plugins are enabled in this image.
Full documentation: https://samtools.github.io/bcftools/howtos/index.html
bcftools mpileup -A -d 200 -B -Q 0 -f {reference_genome} {bam} | bcftools call -mv -Ov -o bcftools_variants/{sample}.vcf