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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
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load miniforge
mamba activate bgen_env

bgenix -g example.bgen -index

References