Difference between revisions of "MaCH: 1000 Genomes Imputation Cookbook"
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=== 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/ MaCH download page]. The most recent set of haplotypes were generated in March 2010 by combining genotype calls generated at the Broad, Sanger and the University of Michigan. In our hands, this March 2010 release is substantially better than previous 1000 Genome Project genotype call sets. | + | 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-2010-03.html MaCH download page]. The most recent set of haplotypes were generated in March 2010 by combining genotype calls generated at the Broad, Sanger and the University of Michigan. In our hands, this March 2010 release is substantially better than previous 1000 Genome Project genotype call sets. |
== Estimating Model Parameters == | == Estimating Model Parameters == | ||
Revision as of 06:47, 4 June 2010
This page documents how to impute 1000 Genome SNPs using MaCH.
Getting Started
Your Own Data
To get started, you will need to store your data in Merlin format pedigree and data files, one per chromosome. For details, of the Merlin file format, see the [http:/www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin tutorial].
Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).
The 1000 Genome pilot project genotypes use NCBI Build 36.
Reference Haplotypes
Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the MaCH download page. The most recent set of haplotypes were generated in March 2010 by combining genotype calls generated at the Broad, Sanger and the University of Michigan. In our hands, this March 2010 release is substantially better than previous 1000 Genome Project genotype call sets.
