Changes

== Optional Phased Haplotypes ==

== Optional Phased Haplotypes ==

For many analyses, but in particular for genotype imputation, it can be very helpful to provide a set of reference haplotypes as input. Reference haplotypes can include genotypes for markers that were not examined in your own sample but which can, often, be inputed based on genotypes at flanking markers. Most commonly, these haplotypes might be derived from a public resource such as the International HapMap Project and, eventually, the 1000 Genomes Project. You can retrieve a current set of phased HapMap format haplotypes from www.hapmap.org/downloads/phasing/.

For many analyses, but in particular for genotype imputation, it can be very helpful to provide a set of reference haplotypes as input. Reference haplotypes can include genotypes for markers that were not examined in your own sample but which can, often, be inputed based on genotypes at flanking markers. Most commonly, these haplotypes might be derived from a public resource such as the International HapMap Project and, eventually, the 1000 Genomes Project.  

 

You can retrieve a current set of phased HapMap format haplotypes from http://hapmap.org/downloads/phasing/2007-08_rel22/phased/.

 

HapMap III phased haplotypes are in different format, you will need to use our converted haplotypes available at http://www.sph.umich.edu/csg/yli/mach/download/HapMap3.r2.b36.html

Phase haplotype information is encoded in two files. The first file (which MACH calls the "snp file") lists the markers in the phased haplotype. The second file (which MACH calls the "haplotype file") lists one haplotype per line. If you retrieved these files from the HapMap website, simply combine the --hapmapFormat option with the --snp option to indicate the name of the HapMap legend file and the --haps option to indicate the name of the file with phased haplotypes. Here is an example:

Phase haplotype information is encoded in two files. The first file (which MACH calls the "snp file") lists the markers in the phased haplotype. The second file (which MACH calls the "haplotype file") lists one haplotype per line. If you retrieved these files from the HapMap website, simply combine the --hapmapFormat option with the --snp option to indicate the name of the HapMap legend file and the --haps option to indicate the name of the file with phased haplotypes. Here is an example: