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, 16:19, 10 August 2011
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| == Pre-Phasing using IMPUTE2 == | | == Pre-Phasing using IMPUTE2 == |
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− | You should now be ready to run the first analysis step, which is to estimate phased haplotypes for each sample. The script below, named ''prototype_phasing_job.sh''(based on the [https://mathgen.stats.ox.ac.uk/impute/prephasing_and_imputation_with_impute2.tgz example script] on the IMPUTE2 website), illustrates how to do this. It requires three parameters (chromosome number, interval start and interval end) and assumes that input data files will in a directory called <code>data_files</code>, with results in <code>results</code> directory and estimated haplotypes in a <code>sampled_haps</code> directory. It has been modified to specify the build 37 recombination map should be used and to include the <code>-allow_large_regions</code> parameter. | + | You should now be ready to run the first analysis step, which is to estimate phased haplotypes for each sample. The script below, named ''prototype_phasing_job.sh''(based on the [https://mathgen.stats.ox.ac.uk/impute/prephasing_and_imputation_with_impute2.tgz example script] on the IMPUTE2 website), illustrates how to do this. It requires three parameters (chromosome number, interval start and interval end) and assumes that input data files will in a directory called <code>data_files</code>, with results in <code>results</code> directory and estimated haplotypes in a <code>sampled_haps</code> directory. It has been modified to specify the build 37 recombination map should be used and to include the <code>-allow_large_regions</code> parameter and to set the effective population size NE=20,000 (as recommended in the IMPUTE2 website for the more recent 1000 Genome Project builds). |
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| <source lang="bash"> | | <source lang="bash"> |
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| ITER=30 | | ITER=30 |
| BURNIN=10 | | BURNIN=10 |
− | NE=11500 | + | NE=20000 |
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| # reference data files | | # reference data files |