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, 23:33, 18 October 2011
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| A typical minimac command line, where the string $chr should be replaced with an appropriate chromosome number, might look like this: | | A typical minimac command line, where the string $chr should be replaced with an appropriate chromosome number, might look like this: |
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− | minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --snpAliases dbsnp134-merges.txt.gz --haps target.hap.$chr.gz --snps target.snps.$chr.gz --prefix chr$chr.imputed | + | minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --snpAliases dbsnp134-merges.txt.gz --haps chr$chr.haps.gz --snps chr.$chr.snps --prefix chr$chr.imputed |
| + | |
| + | chr$chr.haps |
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| A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters: | | A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters: |
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| | Mappings between marker names in earlier versions of dbSNP and the preferred marker names in the current version. The file can be downloaded from [http://www.sph.umich.edu/csg/abecasis/downloads/dbsnp134-merges.txt.gz here]. | | | Mappings between marker names in earlier versions of dbSNP and the preferred marker names in the current version. The file can be downloaded from [http://www.sph.umich.edu/csg/abecasis/downloads/dbsnp134-merges.txt.gz here]. |
| |- | | |- |
− | | <code>--snps target.snps.gz </code> | + | | <code>--snps chr.snps </code> |
| | SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel. | | | SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel. |
| |- | | |- |
− | | <code>--haps target.hap.gz </code> | + | | <code>--haps chr.haps.gz </code> |
| | Phased haplotypes where missing genotypes will be imputed. | | | Phased haplotypes where missing genotypes will be imputed. |
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