gtex.subs

#!/bin/bash
#28-11-2016 MRC-Epid JHZ

TWAS=$1
TWAS2=$2
dir=$3
GTEX_list=$TWAS/GTEX_WEIGHTS.lst

cd $dir
awk -vv=$4 -vs=30 -vFS="," '(NR>=(v-1)*s+1 && NR<=v*s)' $GTEX_list|awk -vTWAS=$TWAS -vTWAS2=$TWAS2 '
{
   wn=sprintf("%s/GTEX_WEIGHTS/%s.wgt",TWAS,$1)
   f=$1
   sub("/","-",f)
# zscore setup
   system(sprintf("echo SNP_ID SNP_Pos Ref_Allele Alt_Allele Z-score > %s.zscore",f))
   system(sprintf("sort -k1,1 %s.map > %s",wn,f))
   system(sprintf("grep -w \"%s\" twas2.txt | join -j1 %s - | sort -k2,2n | awk -f %s/twas2.awk >> %s.zscore",$1,f,TWAS2,f))
# imputation
   system(sprintf("TWAS.sh %s %s.zscore %s",wn,f,f))
   system(sprintf("rm %s %s.zscore",f,f))
}'