MaCH

MaCH is a tool for haplotyping, genotype imputation and disease association analysis developed by Goncalo Abecasis and Yun Li. MaCH was first used to imputed missing genotypes in our FUSION genomewide association study (Scott et al, Science, 2007) and has since been used in the analysis of many other GWAS.

This page includes links to several useful MaCH related resources.

• The main MaCH webpage at http://www.sph.umich.edu/csg/abecasis/MaCH/
• The MaCH download page, with source code, executables and reference haplotype files at http://www.sph.umich.edu/csg/abecasis/MaCH/download/
• The MaCH tutorial at http://www.sph.umich.edu/csg/abecasis/MaCH/tour/
• The MaCH FAQ
• MaCH Options
• Information on MaCH input formats
• 1000 Genomes Imputation Cookbook
• Mach2dat: analyze case-control data with MACH output

Currently, it also includes random notes on input file formats, but these probably need to be cleaned up!