Changes

= 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]). We recommend to use the "ALL (macGT1)" reference haplotypes and to include the <code>-seed</code> parameter, which ensures results can be reproduced by running the script again.

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