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EPACTS (Efficient and Parallelisable Association Container Toolbox) is a versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data, both to scientific analysts and to method developers.

EPACTS is available as a module on Apocrita.


To run the default installed version of EPACTS, simply load the epacts module:

module load epacts
epacts --help
    epacts [command] [options]

For full usage documentation, run epacts --help.

Example job

Serial job

Here is an example job running on 2 cores and 2GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_vmem=1G
#$ -l h_rt=1:0:0

module load epacts

epacts single \
    --vcf input.vcf.gz \
    --ped input.ped  \
    --out out/test \
    --run ${NSLOTS}