dosage_merge.sh

#!/bin/bash




#THe first step may be to just filter down the list of subjects.

#cat  betr/qc1/dos_pts_betr_mix_am-qc.hg19.ch.fl.chr10_009_012.out.dosage.fam vets/qc1/dos_pts_vets_mix_am-qc.hg19.ch.fl.chr10_009_012.out.dosage.fam > test.fam


for files in $(ls betr/qc1/* | grep gz  )
do
 fname=$(echo $files |  awk 'BEGIN{FS="/"}{print $3}' | sed 's/betr/mark/g' )
 betr=$(echo $files)
 minv=$(echo $files | sed 's/betr/minv/g' )
 pts1=$(echo $files | sed 's/betr/pts1/g' )
 psy3=$(echo $files | sed 's/betr/psy3/g' )
 vets=$(echo $files | sed 's/betr/vets/g' )
 
 echo $betr  >> merged_dosages/$fname.mergelist
 echo $minv  >> merged_dosages/$fname.mergelist
 echo $pts1  >> merged_dosages/$fname.mergelist
 echo $psy3  >> merged_dosages/$fname.mergelist
 echo $vets  >> merged_dosages/$fname.mergelist
 
 
/home/maihofer/ricopili/plink --fam test.fam --dosage merged_dosages/$fname.mergelist  list  Zin Zout  --write-dosage --keep mark.subjects --out merged_dosages/"$fname"



done


#sbatch --time 04:00:00 --error errorfile.e --out  outfile.txt 00_merge_data_dosage.sh