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EPACTS

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.

Usage

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

module load epacts
epacts --help
Usage:
    epacts [command] [options]
...

For full usage documentation, run epacts --help.

Example job

Serial job

Here is an example job using 2 cores and 1G RAM per core (2G RAM total) memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_vmem=1G
#$ -l h_rt=240:0:0

module load epacts

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

Reference