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Jump to navigationJump to searchIMPUTE2: 1000 Genomes Imputation Cookbook (view source)
Revision as of 05:19, 11 September 2012
, 05:19, 11 September 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]). 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.
<source lang="bash">
<source lang="bash">
-Ne $NE \
-Ne $NE \
-int $CHUNK_START $CHUNK_END \
-int $CHUNK_START $CHUNK_END \
-o $OUTPUT_FILE \
-o $OUTPUT_FILE \
-allow_large_regions \
-allow_large_regions \
= X-Chromosome Imputation =
= X-Chromosome Imputation =
Please refer to IMPUTE2 example for chromosome X imputation and IMPUTE2 chromosome X options. Please note the difference on the pseudoautosomal and non-pseudoautosomal regions. We recommend not doing pre-phasing for X-chromosome imputation. One reason is that SHAPEIT isn't currently designed to work with X chromosome data (we are not sure whether IMPUTE2 works or not).
Please refer to IMPUTE2 example for chromosome X imputation and IMPUTE2 chromosome X options. Please note the difference on the pseudoautosomal and non-pseudoautosomal regions.
= Association Analysis =
= Association Analysis =
