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, 07:23, 5 August 2011
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| Suppose you plan to run [[Minimac: 1000 Genomes Imputation Cookbook|1000 Genomes Imputation]] using [[MaCH]] and [[minimac]]. Typically, you'd accomplish this by running the two commands: | | Suppose you plan to run [[Minimac: 1000 Genomes Imputation Cookbook|1000 Genomes Imputation]] using [[MaCH]] and [[minimac]]. Typically, you'd accomplish this by running the two commands: |
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− | <source lang="tcsh"> | + | <source lang="bash"> |
| mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 | | mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 |
| minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --haps target.hap.$chr.gz --snps target.snps.$chr.gz --rounds 5 --states 200 --prefix results | | minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --haps target.hap.$chr.gz --snps target.snps.$chr.gz --rounds 5 --states 200 --prefix results |