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

References:

• EPACTS was developed in the Abecasis lab at the University of Michigan. [EPACTS webpage]

• EPACTS Wiki

• Module Name: EPACTS (see the modules page for more information)
• Singlethreaded

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load EPACTS

[user@cn3144 ~]$ cp ${EPACTS_DIR}/1000G_* .

[user@cn3144 ~]$ epacts single --vcf 1000G_exome_chr20_example_softFiltered.calls.vcf.gz   \
       --ped 1000G_dummy_pheno.ped  --min-maf 0.001 --chr 20 --pheno DISEASE \
       --cov AGE --cov SEX --test b.score --anno  --out test --run 2
Detected phenotypes with 2 unique values - 1 and 2 - considering them as binary phenotypes... re-encoding them into 1 and 2
Successfully written phenotypes and 2 covariates across 266 individuals
Processing chromosome 20...
Finished generating EPACTS Makefile
Running 2 parallel jobs of EPACTS
forkExecWait(): make -f /data/user/test.Makefile -j 2
Rscript /usr/local/share/EPACTS/epactsSingle.R --vanilla /usr/local /data/user/test.phe /data/user/test.cov /data/user/test.ind /data/user/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:1-10000000 /data/user/test.20.1.10000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Rscript /usr/local/share/EPACTS/epactsSingle.R --vanilla /usr/local /data/user/test.phe /data/user/test.cov /data/user/test.ind /data/user/1000G_exome_chr20_example_softFiltered.calls.vcf.gz 20:10000001-20000000 /data/user/test.20.10000001.20000000.epacts GT 0.001 1 3 1000000000 0.5 0 FALSE single.b.score
Loading required package: epactsR
Loading required package: epactsR
NOTICE - Reading VCF took 1 seconds
[....]
zcat /data/user/test.epacts.gz | awk '$9 != "NA" { print $0 }' | sort -g -k 9 | head -n 5000 > /data/user/test.epacts.top5000
touch /data/user/test.epacts.OK

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. EPACTS.sh). For example:

#!/bin/bash
set -e

cd /data/$USER
module load EPACTS
cp ${EPACTS_DIR}/1000G_* .
epacts single --vcf  1000G_exome_chr20_example_softFiltered.calls.vcf.gz   \
       --ped  1000G_dummy_pheno.ped    --min-maf 0.001 --chr 20 --pheno DISEASE \
       --cov AGE --cov SEX --test b.score --anno  --out test --run 2

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] EPACTS.sh

Create a swarmfile (e.g. EPACTS.swarm). For example:

epacts single --vcf input1.vcf --ped pheno.ped --out out1 --run 2
epacts single --vcf input2.vcf --ped pheno.ped --out out2 --run 2
epacts single --vcf input3.vcf --ped pheno.ped --out out3 --run 2
epacts single --vcf input4.vcf --ped pheno.ped --out out4 --run 2

Submit this job using the swarm command.

swarm -f EPACTS.swarm [-g #] [-t #] --module EPACTS