gtex-fusion.sge

#!/bin/bash
# 12-7-2017 MRC-Epid JHZ

Rscript=/genetics/bin/Rscript.sh
sumstats=/genetics/bin/FUSION/tests/PGC2.SCZ.sumstats
mkdir $sumstats.tmp
cd $sumstats.tmp
ln -sf /genetics/bin/FUSION/tests/glist-hg19
for GTEx in $(/bin/cat /genetics/bin/FUSION/GTEx.list);do
  for chr in $(seq 22); do
  echo -e "#!/bin/bash\n\
  $Rscript /genetics/bin/fusion_twas/FUSION.assoc_test.R \
  --sumstats $sumstats \
  --weights /genetics/bin/FUSION/GTEx/$GTEx.pos \
  --weights_dir /genetics/bin/FUSION/GTEx \
  --ref_ld_chr /genetics/bin/FUSION/LDREF/1000G.EUR. \
  --chr ${chr} \
  --out $sumstats.tmp/${GTEx}_${chr}.dat;\
  N=`/bin/awk 'END{print FNR-1}' $sumstats.tmp/${GTEx}_${chr}.dat`;\
  /bin/cat $sumstats.tmp/${GTEx}_${chr}.dat|\
  /bin/awk -vN=$N -f /genetics/bin/TWAS-pipeline/gtex-fusion.awk >  $sumstats.tmp/${GTEx}_${chr}.top;\
  $Rscript /genetics/bin/fusion_twas/FUSION.post_process.R \
  --sumstats $sumstats \
  --input $sumstats.tmp/${GTEx}_${chr}.top \
  --out $sumstats.tmp/${GTEx}_${chr}.top.analysis \
  --ref_ld_chr /genetics/bin/FUSION/LDREF/1000G.EUR. --chr ${chr} --plot --locus_win 100000" > sge.sh
  sge "sge.sh"
  done
done