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Revision as of 19:43, 27 August 2012
, 19:43, 27 August 2012→Imputation into Phased Haplotypes - minimac
runon -m 1024 minimac --refHaps ref.hap.$chr.gz --vcfReference \
runon -m 1024 minimac --refHaps ref.hap.$chr.gz --vcfReference \
--haps chr$chr.haps.gz --snps chr.$chr.snps --prefix chr$chr.imputed
--haps chr$chr.haps.gz --snps chr.$chr.snps --prefix chr$chr.imputed
end
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Furthermore, minimac itself can be run in parallel by launching the minimac-omp version. On our cluster 4 cpus per minimac is optimal (--cpus 4).
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foreach chr (`seq 1 22`)
runon -m 1024 minimac-omp --cpus 4 --refHaps ref.hap.$chr.gz --vcfReference \
--haps chr$chr.haps.gz --snps chr.$chr.snps --prefix chr$chr.imputed
end
end
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