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Jump to navigationJump to searchIMPUTE2: 1000 Genomes Imputation Cookbook (view source)
Revision as of 23:12, 24 July 2012
, 23:12, 24 July 2012→Content
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.
