Changes

This page documents how to carry out imputation using [http://mathgen.stats.ox.ac.uk/impute/impute_v2.html IMPUTE2] software (developed by Jonathan Marchini and Bryan Howie) and 1000 Genomes reference panel haplotypes.

This page documents how to carry out imputation using [http://mathgen.stats.ox.ac.uk/impute/impute_v2.html IMPUTE2] software (developed by Jonathan Marchini and Bryan Howie) and 1000 Genomes reference panel haplotypes.

For information on how to carry out 1000 Genomes Imputation using [[Minimac]], see [[Minimac: GIANT 1000 Genomes Imputation Cookbook]].

For information on how to carry out 1000 Genomes Imputation using [[Minimac]], see [[Minimac:_1000_Genomes_Imputation_Cookbook]].

As of now, the most recent version of the 1000 Genome Project haplotypes are the Phase I Integrated release haplotypes (available in IMPUTE2 format from [http://mathgen.stats.ox.ac.uk/impute/data_download_1000G_phase1_integrated.html this link]). This haplotype set is more complete and more accurate than prior 1000 Genome Project haplotypes and is recommended for all imputation based analyses.

As of now, the most recent version of the 1000 Genome Project haplotypes are the Phase I Integrated release haplotypes (available in IMPUTE2 format from [http://mathgen.stats.ox.ac.uk/impute/data_download_1000G_phase1_integrated.html this link]). This haplotype set is more complete and more accurate than prior 1000 Genome Project haplotypes and is recommended for all imputation based analyses.

= 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 =