Changes

There are two choices for imputation step: imputing from best-guess haplotypes and imputing from a sample of alternate haplotype configurations.

There are two choices for imputation step: imputing from best-guess haplotypes and imputing from a sample of alternate haplotype configurations.

Imputing from best-guess haplotypes uses the best-guess haplotypes is much faster and we recommend it. Below is a lightly modified version of script “prototype_imputation_job_best_guess_haps.sh” that accomplishes imputation. The script has been modified to reference the most recent set of 1000 Genome Haplotypes (currently, the interim Phase I haplotypes [http://mathgen.stats.ox.ac.uk/impute/data_download_1000G_phase1_interim.html available from the IMPUTE2 website]) and to include the <code>-seed</code> which ensures results can be reproduced by running the script again.

Imputing from best-guess haplotypes is much faster and we recommend it. 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 IMPUTE2 examples. This version has been modified to reference the most recent set of 1000 Genome Haplotypes (currently, the interim Phase I haplotypes [http://mathgen.stats.ox.ac.uk/impute/data_download_1000G_phase1_interim.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.

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