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900 bytes added
, 07:13, 4 June 2010
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− | 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$chr.parameters >& chr$chr.model.log &
| + | --greedy -r 100 -o chr$chr.parameters --compact >& chr$chr.model.log & |
| + | |
| + | end |
| + | </source> |
| + | |
| + | == 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> |