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Revision as of 13:12, 30 May 2012
, 13:12, 30 May 2012→Imputation
= Imputation =
= Imputation =
Below is a lightly modified version of script “prototype_imputation_job_best_guess_haps.sh” that accomplishes imputation. The original script is included in the package of [http://mathgen.stats.ox.ac.uk/impute/prephasing_and_imputation_with_impute2.tgz IMPUTE2 examples]. This version has been modified to reference the most recent set of 1000 Genome Haplotypes (currently, the Phase I integrated haplotypes [http://mathgen.stats.ox.ac.uk/impute/data_download_1000G_phase1_integrated.html available from the IMPUTE2 website]) and to include the <code>-seed</code> parameter, which ensures results can be reproduced by running the script again.
Below is a lightly modified version of script “prototype_imputation_job_best_guess_haps.sh” that accomplishes imputation. The original script is included in the package of [http://mathgen.stats.ox.ac.uk/impute/prephasing_and_imputation_with_impute2.tgz IMPUTE2 examples]. This version has been modified to reference the most recent set of 1000 Genome Haplotypes (currently, the Phase I integrated haplotypes [http://mathgen.stats.ox.ac.uk/impute/data_download_1000G_phase1_integrated.html available from the IMPUTE2 website]) and to include the <code>-seed</code> parameter, which ensures results can be reproduced by running the script again.
Filtering Option -filt_rules_l is used in this example to remove reference SNPs with MAF=0 in European reference panel (for example, a European cohort).
Filtering Option -filt_rules_l is used in this example to remove reference SNPs with MAF=0 in European reference panel (for example, a European cohort).
The syntax for starting each of these jobs would be similar for the phasing jobs and, again, you should use a suitable grid or cluster engine to submit multiple jobs in parallel.
The syntax for starting each of these jobs would be similar for the phasing jobs and, again, you should use a suitable grid or cluster engine to submit multiple jobs in parallel.
= X-Chromosome Imputation =
= X-Chromosome Imputation =
