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 running on 2 cores and 2GB of memory:
#!/bin/bash
#$ -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}