angsd

Download        : docker pull ghcr.io/autamus/angsd
Compressed Size : 287MB

Description

Angsd is a program for analysing NGS data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.

Usage

Pull (Download)

To download the latest version of angsd run,

docker pull ghcr.io/autamus/angsd:latest

or to download a specific version of angsd run,

docker pull ghcr.io/autamus/angsd:0.933

Run

To run the container as an application run,

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

or to run the container in an interactive session run,

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

Mounting volumes between the container and your machine

To access files from your machine within the angsd 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/angsd angsd /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 angsd container here.