1,555
edits
Changes
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awk '{ if ($1 == "M") print $2; }' < chr1.dat > chr1.snps
awk '{ if ($1 == "M") print $2; }' < chr1.dat > chr1.snps
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --prefix chr1.haps
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --prefix chr1.haps
minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps chr1.haps.gz --snps chr1.snps --rounds 5 --states 200 --prefix imputation-results
minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps chr1.haps.gz --snps chr1.snps --rounds 5 --states 200 --prefix chr1.imputed
</source>
</source>
# Phase each chunk in parallel
# Phase each chunk in parallel
foreach chunk (chunk*-chr1.dat)
foreach chunk (chunk*-chr1.dat)
mach1 -d $chunk -p chr1.ped --rounds 20 --states 200 --phase --prefix ${chunk:r}.haps >& ${chunk:r}-mach.log &
mach1 -d $chunk -p chr1.ped --rounds 20 --states 200 --phase --prefix ${chunk:r} >& ${chunk:r}-mach.log &
end
end
wait
wait
minimac --autoClip autoChunk-chr1.dat \
minimac --autoClip autoChunk-chr1.dat \
--refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --rounds 5 --states 200 \
--refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --rounds 5 --states 200 \
--haps ${chunk:r}.haps.gz --snps ${chunk}.snps --prefix ${chunk:r}-results >& ${chunk:r}-minimac.log &
--haps ${chunk:r}.gz --snps ${chunk}.snps --prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &
end
end
wait
wait
