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| Reduce memory use at the cost of approximately doubling runtime. This option is recommended for most GWAS scale datasets and computing platforms.
| Reduce memory use at the cost of approximately doubling runtime. This option is recommended for most GWAS scale datasets and computing platforms.
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== Imputation into Phased Haplotypes ==
== Imputation into Phased Haplotypes ==
=== Reference Haplotypes ===
=== Reference Haplotypes ===
Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-08.html MaCH download page]. The most recent set of haplotypes are based on genotype calls from the August 2010 data freeze.
Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MACH/download/ MaCH download page]. As of this writing, the most recent set of haplotypes are based on genotype calls were generated in May 2011 and are an interim analysis of Project's Phase I data.
=== Imputation quality evaluation ===
=== Imputation quality evaluation ===
These statistics can be found in the .info file
These statistics can be found in the .info file
=== Additional Sources of Information ===
If the combination of MaCH and Minimac still runs too slowly for you, and you have access to a multi-processor compute cluster, you can look at [[ChunkHaplotypes]] page to learn how to conveniently split each chromosome into multiple segments that can be analyzed in parallel.
If you are especially interested in 1000 Genomes Imputation, then you should look at the [[Minimac: 1000 Genomes Imputation Cookbook]].
== X Chromosome Imputation ==
== X Chromosome Imputation ==
