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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 imputation-results
</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 &
mach1 -d $chunk -p chr1.ped --rounds 20 --states 200 --phase --prefix ${chunk:r}.haps >& ${chunk:r}-mach.log &
end
end
wait
# Impute each chunk in parallel
# Impute each chunk in parallel
foreach chunk (chunk*-chr1.dat)
foreach chunk (chunk*-chr1.dat)
minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps ${chunk:r}.haps.gz --snps ${chunk:r}.snps --rounds 5 --states 200 --prefix ${chunk:r}-results
minimac --autoClip autoChunk-chr1.dat \
--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 &
end
end
wait
</source>
The ''autoChunk'', generated by the ChunkChromosome program, tells minimac what are the markers of interest for each chunk. This allows chunks to overlap (which improves accuracy near the edges) but still ensures that each marker is only imputed once.
== Download ==
== Download ==
