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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
</source>
</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.
The ''autoChunk'' file, 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 ==
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.
