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''ChunkChromosome'' is a helper utility for [[minimac]] and [[MaCH]]. It can be used to facilitate analyses of very large datasets in overlapping slices.
''ChunkChromosome'' is a helper utility for [[minimac]] and [[MaCH]]. It can be used to facilitate analyses of very large datasets in overlapping slices. For information on how to put the resulting chunks back together, see [[Ligate Minimac|this page]].
== Parameters ==
== Parameters ==
awk '{ if ($1 == "M") print $2; }' < chr1.dat > chr1.snps
awk '{ if ($1 == "M") print $2; }' < chr1.dat > chr1.snps
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --prefix chr1.haps
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --prefix chr1.haps
minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps chr1.haps.gz --snps chr1.snps --rounds 5 --states 200 --prefix imputation-results
minimac --refHaps 1000genomes.chr1.haps.gz --refSnps 1000genomes.chr1.snps --haps chr1.haps.gz --snps chr1.snps --rounds 5 --states 200 --prefix chr1.imputed
</source>
</source>
<source lang="bash">
<source lang="bash">
ChunkChromosome -d chr1.dat
#!/bin/tcsh
@ length = 2500
@ overlap = 500
# Estimate haplotypes for all individuals, in 2500 marker chunks, with 500 marker overhang
foreach chr (`seq 1 22`)
ChunkChromosome -d chr$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
== Download ==
== Download ==
You can download source code for the ChunkChromosome program from [here]. After downloading it, unpack the archive and use Make to compile the tool.
You can download source code for the ChunkChromosome program in a tar-ball archive [http://csg.sph.umich.edu//cfuchsb/generic-ChunkChromosome-2014-05-27.tar.gz generic-ChunkChromosome-2014-05-27.tar.gz]. After downloading it, unpack the archive and use Make to compile the tool.
