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A suite of tools to analyse binary GEN files.

BGEN is available as a module on Apocrita.


To run the default installed version of BGEN, simply load the bgen module:

module load bgen
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:

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

module load bgen

bgenix -g example.bgen -index