bcftools

Download        : docker pull ghcr.io/autamus/bcftools
Compressed Size : 164MB

Description

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.

Usage

Pull (Download)

To download the latest version of bcftools run,

docker pull ghcr.io/autamus/bcftools:latest

or to download a specific version of bcftools run,

docker pull ghcr.io/autamus/bcftools:1.11

Run

To run the container as an application run,

docker run --rm ghcr.io/autamus/bcftools bcftools --version

or to run the container in an interactive session run,

docker run -it --rm ghcr.io/autamus/bcftools bash

Mounting volumes between the container and your machine

To access files from your machine within the bcftools container you’ll have to mount them using the -v external/path:internal/path option.

For example,

docker run -v ~/Documents/Data:/Data ghcr.io/autamus/bcftools bcftools /Data/myData.csv

which will mount the ~/Documents/Data directory on your computer to the /Data directory within the container.

HPC

If you’re looking to use this container in an HPC environment we recommend using Singularity-HPC to use the container just as any other module on the cluster. Check out the SHPC bcftools container here.