Skip to content

BGEN

A suite of tools to analyse binary GEN files.

Conda installation

BGEN can be installed from the Conda Forge Anaconda channel by loading the Miniforge module and then creating a Conda environment and installing BGEN into it (output below truncated):

$ module load miniforge
$ mamba create --quiet --yes --name bgen_env
$ mamba activate bgen_env
(bgen_env) $ mamba install conda-forge::bgenix

Looking for: ['conda-forge::bgenix']
...
  Updating specs:

   - conda-forge::bgenix
...
Confirm changes: [Y/n] Y
...
Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Usage

To run the Conda installed version of BGEN, simply load the miniforge module and activate the Conda environment you installed it into:

$ module load miniforge
$ mamba activate bgen_env
(bgen_env) $ bgenix -help

Usage: bgenix <options>

For usage documentation, run bgenix -help.

The BGEN suite contains single threaded applications

All tools in the BGEN suite do not provide support for multi-threading so please only request 1 core in your submission scripts. Any additional cores requested will be unused and wasted.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory to build an index for the specified BGEN file:

#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=1G   # Request 1GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load miniforge
mamba activate bgen_env

bgenix -g example.bgen -index

References