IMPUTE_LOOP_PHASE1_STEP3.sh

#!/bin/sh
#1 - chromosome number
#2 total length of chr
#3 file name
for i in `seq 0 $2` 
do
interval=`echo $i'e6 '$(($i +1))'e6'`
command=`echo ./impute2 -known_haps_g "$3"_CHR"$1".haps -h /srv/gsfs0/projects/mignot/IMPUTE_REFERENCE_PHASE1/ALL.chr"$1".integrated_phase1_v3.20101123.snps_indels_svs.genotypes.nomono.haplotypes.gz -l /srv/gsfs0/projects/mignot/IMPUTE_REFERENCE_PHASE1/ALL.chr"$1".integrated_phase1_v3.20101123.snps_indels_svs.genotypes.nomono.legend.gz -m /srv/gsfs0/projects/mignot/IMPUTE_REFERENCE_PHASE1/genetic_map_chr"$1"_combined_b37.txt -int "$interval" -buffer 500 -Ne 20000 -o CHR"$1"_"$3"."$i"`
touch tmpchr"$1".$i.sh
chmod 755 tmpchr"$1".$i.sh
cat > tmpchr"$1".$i.sh <<- EOF
#!/bin/bash
#$ -N EM_$i.chr"$1"
#$ -hold_jid shapeit_array
#$ -l h_vmem=10g
#$ -l h_rt=6:00:00
#$ -w e
$command
EOF
qsub -V -cwd tmpchr"$1".$i.sh
rm tmpchr"$1".$i.sh
done