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, 07:50, 19 September 2011
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| A typical minimac command line might look like this: | | A typical minimac command line might look like this: |
| | | |
− | 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 --snpAlias dbsnp134-merged.txt.gz --haps target.hap.$chr.gz --snps target.snps.$chr.gz --prefix results |
| | | |
| 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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| | <code>--refHaps ref.hap.gz </code> | | | <code>--refHaps ref.hap.gz </code> |
| | Reference haplotypes (e.g. from [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page]) | | | Reference haplotypes (e.g. from [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page]) |
| + | |- |
| + | | <code>--snpAlias dbsnp134-merged.txt.gz</code> |
| + | | 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 target.snps.gz </code> |
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| end | | end |
| </source> | | </source> |
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| == Further Time Savings == | | == Further Time Savings == |