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.
Info
Module Name
bcftools
Last Updated On
11/14/2023
Support Level
Primary Support
Software Access Level
Open Access
Home Page
Documentation
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.
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 small,large,ram256g,ram1t
module load bcftools/1.6
wget https://public.s3.msi.umn.edu/reframe/sw/bcftools/example.vcf
bcftools query -l example.vcf
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
Agate Modules
Default
1.16-gcc-8.2.0-5d4xg4y
Other Modules
1.16-gcc-8.2.0-5d4xg4y, 1.10.2, 1.9, 0.2.0, 1.2, 1.6
Mangi Modules
Default
1.16-gcc-8.2.0-5d4xg4y
Other Modules
1.16-gcc-8.2.0-5d4xg4y, 1.10.2, 1.9, 0.2.0, 1.2, 1.6
Mesabi Modules
Default
1.16-gcc-8.2.0-5d4xg4y
Other Modules
1.16-gcc-8.2.0-5d4xg4y, 1.10.2, 1.9, 0.2.0, 1.2, 1.6