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Revision as of 23:05, 10 February 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.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.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
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:
| Optionally, a string that is used to help generate output file names.
| Optionally, a string that is used to help generate output file names.
|}
|}
Again, you can speed-up things by running this step in parallel and in our cluster we'd use:
<source lang="text">
foreach chr (`seq 1 22`)
runon -m 1024 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
end
</source>
