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<source lang="bash">
<source lang="bash">
ChunkChromosome -d chr1.dat
#!/bin/tcsh
@ length = 2500
@ overlap = 500
# Estimate haplotypes for all individuals, in 2500 marker chunks, with 500 marker overhang
foreach chr (`seq 1 22`)
ChunkChromosome -d chr$chr.dat -n $length -o $overlap
foreach chunk (chunk*-chr$chr.dat)
mach -d $chunk -p chr$chr.ped --prefix ${chunk:r} \
--rounds 20 --states 200 --phase --sample 5 >& ${chunk:r}-mach.log &
end
end
end
wait
wait
# Impute each chunk in parallel
# Impute into phased haplotypes
foreach chunk (chunk*-chr1.dat)
foreach chr (`seq 1 22`)
foreach chunk (chunk*-chr$chr.dat)
set haps = /data/1000g/hap/all/20101123.chr$chr.hap.gz
set snps = /data/1000g/snps/chr$chr.snps
minimac --refHaps $haps --refSnps $snps --rounds 5 --states 200 \
--haps ${chunk:r}.gz --snps ${chunk}.snps --autoClip autoChunk-chr$chr.dat \
--prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &
end
end
end
wait
wait
