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417 bytes added
, 19:43, 27 August 2012
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| 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 |
| + | </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 | | end |
| </source> | | </source> |