SNPTEST GWAS script

run_snptest.sh

#!/bin/bash

#PBS -N sleepgwas
#PBS -o sleepsnptest-output
#PBS -e sleepsnptest-error
#PBS -t 1-22
#PBS -l walltime=24:00:00
#PBS -l nodes=1:ppn=2
#PBS -S /bin/bash

set -e

echo "Running on ${HOSTNAME}"

if [ -n "${1}" ]; then
  echo "${1}"
  PBS_ARRAYID=${1}
fi

i=${PBS_ARRAYID}

module add apps/snptest.2.5.0


genfile="/panfs/panasas01/shared/alspac/studies/latest/alspac/genetic/variants/arrays/gwas/imputed/1000genomes/released/27Feb2015/data/genotypes/dosage/data_chr${i}"
samplefile="/panfs/panasas01/shared/alspac/studies/latest/alspac/genetic/variants/arrays/gwas/imputed/1000genomes/released/27Feb2015/data/data.sample"

# Change this file to point to where you want
outfile="${HOME}/results_chr${i}"

snptest_v2.5 \
	-data ${genfile} ${samplefile} \
	-missing_code -9 \
	-pheno plink_pheno \
	-cov_all \
	-use_raw_phenotypes \
	-frequentist 1 \
	-method em \
	-o ${outfile}