Changes

# Impute into phased haplotypes

# Impute into phased haplotypes

foreach chr (`seq 1 22`)

foreach chr (`seq 1 22`)

   minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --haps chr$chr.haps.gz --snps chr$chr.snps --rounds 5 --states 200 --prefix chr$chr.imputed >& chr$chr-minimac.log &

   minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --snpAliases dbsnp134-merges.txt.gz \

          --haps chr$chr.haps.gz --snps chr$chr.snps --prefix chr$chr.imputed >& chr$chr-minimac.log &

end

end

wait

wait

       set snps = /data/1000g/snps/chr$chr.snps

       set snps = /data/1000g/snps/chr$chr.snps

       minimac --refHaps $haps --refSnps $snps --rounds 5 --states 200 \

       minimac --refHaps $haps --refSnps $snps --snpAliases dbsnp134-merges.txt.gz \

               --haps ${chunk:r}.gz --snps ${chunk}.snps  --autoClip autoChunk-chr$chr.dat  \

               --haps ${chunk:r}.gz --snps ${chunk}.snps  --autoClip autoChunk-chr$chr.dat  \

               --prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &

               --prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &