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Minimac: 1000 Genomes Imputation Cookbook

417 bytes added, 19:43, 27 August 2012
Imputation into Phased Haplotypes - minimac
runon -m 1024 minimac --refHaps ref.hap.$chr.gz --vcfReference \
--haps chr$chr.haps.gz --snps chr.$chr.snps --prefix chr$chr.imputed
end
</source>
 
 
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).
 
<source lang="text">
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
</source>
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