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Revision as of 08:08, 19 September 2011
, 08:08, 19 September 2011→Imputation into Phased Haplotypes - minimac
A typical minimac command line might look like this:
A typical minimac command line, where the string $chr should be replaced with an appropriate chromosome number, might look like this:
minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --snpAlias dbsnp134-merged.txt.gz --haps target.hap.$chr.gz --snps target.snps.$chr.gz --prefix results
minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --snpAliases dbsnp134-merges.txt.gz --haps target.hap.$chr.gz --snps target.snps.$chr.gz --prefix results$chr
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:
| 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>
| <code>--snpAliases 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].
| 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].
|-
|-
foreach chr (`seq 1 22`)
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
runon -m 1024 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 results$chr
end
end
