SGE job array for phasing GWAS data with shapeit2

shapeit2_phasing_array.sh

#!/bin/bash
## Inherit user environment from the login node
#$ -V
## Use the current directory as the working directory for SGE output and determining paths to files
#$ -cwd
## Request parallel environment and a number cores
#$ -pe smp.pe 12
##
## create an array
#$ -t 1-22
##
##

export OMP_NUM_THREADS=$NSLOTS

# link to latest version of shapeit2
shapeit2="/mnt/iusers01/jw01/jw01-shared-resources/shapeit2/bin/shapeit.v2.r727.linux.x64"

# input files
CHR=${SGE_TASK_ID}
STUDY_DATA="phasing/data/Immunochip_PsA_hg19_refAligned_chr${CHR}"
MAP="/mnt/iusers01/jw01/jw01-shared-resources/shapeit2/genetic_maps_b37/genetic_map_chr${CHR}_combined_b37.txt"

# out files
OUT_FILE="phasing/output/Immunochip_PsA_hg19_chr${CHR}"

$shapeit2 -B $STUDY_DATA \
         -M ${MAP} \
         -O ${OUT_FILE}.haps.gz ${OUT_FILE}.sample \
         -T $NSLOTS \
         -L  ${OUT_FILE}.log