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Revision as of 09:14, 5 August 2011
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This page documents how to impute 1000 Genome SNPs using [[Minimac]], which is typically the preferred approach for imputation using large reference panels such as the 1000 Genomes data. For information on how to carry out 1000 Genomes Imputation using [[MaCH]], see [[MaCH: 1000 Genomes Imputation Cookbook]]. For pointers on how to carry out 1000 Genomes Imputation using [[IMPUTE2]], see [[IMPUTE2: 1000 Genomes Imputation Cookbook]].
This page documents how to impute 1000 Genome SNPs using [[Minimac]], which is typically the preferred approach for imputation using large reference panels such as the 1000 Genomes data. For information on how to carry out 1000 Genomes Imputation using [[MaCH]], see [[MaCH: 1000 Genomes Imputation Cookbook]]. For pointers on how to carry out 1000 Genomes Imputation using [[IMPUTE2]], see [[IMPUTE2: 1000 Genomes Imputation Cookbook]].
Before reading this tutorial, you might find it useful to spend a few minutes reading through the main [[Minimac]] documentation.
== Should I use MaCH or minimac? ==
== Should I use MaCH or minimac? ==
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== Further Time Savings ==
The recipe above imputes whole chromosomes, one a time. A further time savings is possible by imputing chromosomes in chunks, a process that can be facilitated using the [[ChunkChromosome]] tool.
== X Chromosome Imputation ==
== X Chromosome Imputation ==
