h2.sb

#!/bin/bash

#SBATCH --account CARDIO-SL0-CPU
#SBATCH --ntasks=1
#SBATCH --job-name=_h2
#SBATCH --time=8:00:00
#SBATCH --cpus-per-task=1
#SBATCH --partition=cardio
#SBATCH --mem=128800
#SBATCH --array=1-22
#SBATCH --output=/rds/user/jhz22/hpc-work/work/_prune_%A_%a.out
#SBATCH --error=/rds/user/jhz22/hpc-work/work/_prune_%A_%a.err
#SBATCH --export ALL

#SBATCH --account CARDIO-SL0-CPU
#SBATCH --ntasks=1
#SBATCH --job-name=_h2
#SBATCH --time=8:00:00
#SBATCH --cpus-per-task=1
#SBATCH --partition=cardio
#SBATCH --mem=128800
#SBATCH --array=1-92
#SBATCH --output=/rds/user/jhz22/hpc-work/work/_h2_%A_%a.out
#SBATCH --error=/rds/user/jhz22/hpc-work/work/_h2_%A_%a.err
#SBATCH --export ALL

. /etc/profile.d/modules.sh

export chr=${SLURM_ARRAY_TASK_ID}

function prune()
{
  module load plink/2.00-alpha
  cd ${INF}/h2
  plink2 --bfile ${INF}/INTERVAL/per_chr/interval.imputed.olink.chr_${chr} \
         --chr ${chr} \
         --geno 0.1 --mind 0.1 --maf 0.005 --indep-pairwise 1000kb 1 0.8 --out ${chr}
  if [ ${chr} -eq 19 ]; then
     sort ${chr}.prune.in | \
     join -v1 - ${INF}/work/NLRP2 > ${chr}.prune
  else
     sort ${chr}.prune.in > ${chr}.prune
  fi
# rm ${chr}.prune.in ${chr}.prune.out
  plink2 --bfile ${INF}/INTERVAL/per_chr/interval.imputed.olink.chr_${chr} --extract ${chr}.prune --make-bed --out ${chr}
  cd -
}

function h2()
# --reml-alg 1 for 47,91
{
  export s=${INF}/INTERVAL/o5000-inf1-outlier_in-r2.sample
  export p=$(cut -d' ' -f29- ${s} | head -1 | sed 's/ /\n/g' | awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]{split($1,a,"__"); print a[1]}')

  cd ${INF}/h2
  gcta64 --reml \
         --grm INTERVAL \
         --pheno INTERVAL.pheno \
         --covar INTERVAL.covar \
         --qcovar INTERVAL.qcovar \
         --mpheno ${SLURM_ARRAY_TASK_ID} \
         --thread-num 2 \
         --out ${p}
  cd -
}

#prune
h2