INTERVAL-rma.sb

#!/bin/bash

#SBATCH --ntasks=1
#SBATCH --job-name=_rma
#SBATCH --time=8:00:00
#SBATCH --partition=medium
#SBATCH --mem=128800
#SBATCH --array=1-92%2
#SBATCH --output=INTERVAL/_rma_%A_%a.out
#SBATCH --error=INTERVAL/_rma_%A_%a.err
#SBATCH --export ALL

. /etc/profile.d/modules.sh
module load default-cardio
module load slurm
module load use.own
module load gcc/5.2.0

export TMPDIR=/scratch/jhz22/tmp
export rt=/home/jhz22/INF
export prot=$(awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]{print $1}' work/inf1.tmp)
export p=$prot
export bed=tryggve/EURLD-no-high-LD-regions-hg19.bed

(
  echo -e \#chrom "\t" Start "\t" End "\t" SNP "\t" A1 "\t" A2 "\t" freq "\t" b "\t" se "\t" p "\t" N
  gunzip -c $rt/sumstats/INTERVAL/INTERVAL.${p}.gz | \
  awk 'NR>1 && $14>50' | \
  sort -k1,1n -k2,2 | \
  awk -vOFS="\t" '{print "chr" $2, $3-1, $3, $1, $6, $7, $8, $9, $10, $11, $5}'
) | \
bedtools intersect -a $bed -b - -loj | \
cut -f4,8-15 > INTERVAL/${p}.rma

(
  echo SNP A1 A2 freq b se p N
  awk "!/NA/ {print $2, $3, $4, $5, $6, $7, $8, $9}" INTERVAL/${p}.rma
) > INTERVAL/${p}.ma'