# bcftools

## Summary

+ **Module Name:** bcftools
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [https://samtools.github.io/bcftools/](https://samtools.github.io/bcftools/)

## Software Description

BCFtools are meant as a faster replacement for most of the perl
VCFTools commands. Bcftools is a set of utilities that manipulate
variant calls in the Variant Call Format (VCF) and its binary
counterpart BCF. All commands work transparently with both VCFs and
BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF,
bgzipped VCF and BCF with filetype detected automatically even when
streaming from a pipe. Indexed VCF and BCF will work in all situations.
Un-indexed VCF and BCF and streams will work in most, but not all
situations. Bcftools is designed to work on a stream. It regards an
input file \"-\" as the standard input (stdin) and outputs to the
standard output (stdout). Several commands can thus be combined with
Unix pipes.
## General Linux

To load this module for use in a Linux environment, you can run the command:

	module load bcftools

Depending on where you are working, there may be more than one version of bcftools available.
To see which modules are available for loading you can run:

	module avail bcftools
## Slurm Example


	#!/bin/bash
	#SBATCH --job-name="rfm_RunBcftoolsTest_job"
	#SBATCH --ntasks=1
	#SBATCH --ntasks-per-node=1
	#SBATCH --output=rfm_RunBcftoolsTest_job.out
	#SBATCH --error=rfm_RunBcftoolsTest_job.err
	#SBATCH --time=0:10:0
	#SBATCH -p msismall
	module load bcftools/1.6
	wget https://public.s3.msi.umn.edu/reframe/sw/bcftools/example.vcf
	bcftools query -l example.vcf