MaCH: 1000 Genomes Imputation Cookbook

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.

Estimating Model Parameters

The first step for genotype imputation analyses using MaCH is to build a model that relates your dataset to a reference set of haplotypes. This model will include information on the length of haplotype stretches shared between your sample and the reference panel (in a .rec file) and information on the similarity of marker genotypes between your sample and the reference panel (in a .err file). The contents of the second file reflect the combined effects of genotyping error and differences in genotyping assays between the two samples.