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Revision as of 09:40, 30 May 2012
, 09:40, 30 May 2012→Further Time Savings
</source>
</source>
A modified script, using [[ChunkChromosome]] would look like this:
A modified script, using [[ChunkChromosome]] would look like this (chr:pos GWAS SNP IDs):
<source lang="bash">
<source lang="bash">
minimac --refHaps $haps --refSnps $snps --vcfReference \
minimac --refHaps $haps --refSnps $snps --vcfReference \
--haps ${chunk:r}.gz --snps ${chunk}.snps --autoClip autoChunk-chr$chr.dat \
--prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &
end
end
wait
</source>
Using [[ChunkChromosome]] would look like this (rs GWAS SNP IDs):
<source lang="bash">
#!/bin/tcsh
@ length = 2500
@ overlap = 500
# Estimate haplotypes for all individuals, in 2500 marker chunks, with 500 marker overhang
foreach chr (`seq 1 22`)
ChunkChromosome -d chr$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 >& ${chunk:r}-mach.log &
end
end
wait
# Impute into phased haplotypes
foreach chr (`seq 1 22`)
foreach chunk (chunk*-chr$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 --vcfReference --rs --snpAliases dbsnp134-merges.txt.gz \
--haps ${chunk:r}.gz --snps ${chunk}.snps --autoClip autoChunk-chr$chr.dat \
--haps ${chunk:r}.gz --snps ${chunk}.snps --autoClip autoChunk-chr$chr.dat \
--prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &
--prefix ${chunk:r}.imputed >& ${chunk:r}-minimac.log &
