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Revision as of 07:13, 4 June 2010
, 07:13, 4 June 2010→Selecting a Subset of Samples
EOF
EOF
runon mach -d chr$chr.rand200.dat -p chr$chr.rand200.ped -s CEU.1000G/chr$chr.snps -h CEU.1000G/chr$chr.hap \
runon -m 4096 mach -d chr$chr.rand200.dat -p chr$chr.rand200.ped -s CEU.1000G/chr$chr.snps -h CEU.1000G/chr$chr.hap \
--greedy -r 100 -o chr$chr.parameters --compact >& chr$chr.model.log &
end
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== Imputation ==
Once model parameters have been estimated, you are ready to impute. This step should be comparatively fast, at least on a per individual basis.
Your command line should look like this:
mach -d chr1.dat -p chr1.ped -s CEU.1000G/chr1.snps -h CEU.1000G/chr1.hap \
--errorMap chr1.parameters.erate --crossoverMap chr1.parameters.rec \
--compact --greedy --autoFlip --mle --mldetails >& chr$chr.impute.log
Again, you should be able to run this step in parallel and in our cluster we'd use:
<source lang="text">
foreach chr (`seq 1 22`)
runon -m 4096 mach -d chr$chr.dat -p chr$chr.ped -s CEU.1000G/chr$chr.snps -h CEU.1000G/chr$chr.hap \
--errorMap chr$chr.parameters.erate --crossoverMap chr$chr.parameters.rec \
--compact --greedy --autoFlip --mle --mldetails >& chr$chr.impute.log
end
end
</source>
</source>
