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Revision as of 10:05, 5 August 2011
, 10:05, 5 August 2011→Further Time Savings
== Further Time Savings ==
== Further Time Savings ==
The recipe above imputes whole chromosomes, one a time. A further time savings is possible by imputing chromosomes in chunks, a process that can be facilitated using the [[ChunkChromosome]] tool.
The recipe above imputes whole chromosomes, one a time. A further time savings is possible by imputing chromosomes in chunks, a process that can be facilitated using the [[ChunkChromosome]] tool.
Recall that the original analysis script might have looked like this:
<source lang="bash">
#!/bin/tcsh
# Build SNP lists for each chromosome
foreach chr (`seq 1 22`)
awk '{ if ($1 == "M") print $2; }' < chr${chr}.dat > chr${chr}.snps
end
# Estimate haplotypes for all individuals, one chromosome at a time
foreach chr (`seq 1 22`)
mach -d chr$chr.dat -p chr$chr.ped --rounds 20 --states 200 --phase --sample 5 --prefix chr$chr.haps &
end
wait
# Impute into phased haplotypes
foreach chr (`seq 1 22`)
minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --haps chr$chr.haps.gz --snps chr$chr.snps --rounds 5 --states 200 --prefix chr$chr.imputed &
end
wait
</source>
<source lang="bash">
#!/bin/tcsh
@ length = 2500
@ overlap = 500
# Estimate haplotypes for all individuals, in 5000 marker chunks, with 500 marker overhang
foreach chr (`seq 1 22`)
ChunkChromosome -d chr$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 >& ${chunk:r}-mach.log &
end
end
wait
# Impute into phased haplotypes
foreach chr (`seq 1 22`)
foreach chunk (chunk*-chr$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
wait
</source>
== X Chromosome Imputation ==
== X Chromosome Imputation ==
