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, 17:51, 26 April 2010
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| This file tells us that fields 6-8 in the pedigree file store genotypes for SNP1-3 correspondingly. Note again that the list of SNPs must be in their physical order along the chromosomes. | | This file tells us that fields 6-8 in the pedigree file store genotypes for SNP1-3 correspondingly. Note again that the list of SNPs must be in their physical order along the chromosomes. |
| + | |
| + | |
| + | <strong>Optional Input files</strong><br> |
| + | External (e.g., HapMap) data (snp and haplotype files) are optional. |
| + | Mach 1.0 accepts two different formats: MACH format or HapMap format. |
| + | HapMap format files can be downloaded from: |
| + | |
| + | http://hapmap.org/downloads/phasing/2006-07_phaseII/phased/ |
| + | |
| + | or |
| + | |
| + | http://hapmap.org/downloads/phasing/2007-08_rel22/phased/ |
| + | |
| + | When using HapMap format files, turn on --hapmapFormat option. |
| + | |
| + | MACH format HapMap SNP File |
| + | --------------------------- |
| + | One line per SNP and one field (marker name) only. |
| + | |
| + | For example: |
| + | |
| + | marker1 |
| + | marker2 |
| + | ... |
| + | |
| + | MACH format HapMap Haplotype File |
| + | --------------------------------- |
| + | One line per haplotype. |
| + | Heading identification fields are optional. |
| + | Each non-haplotype/heading field shall not start with a numeric digit. |
| + | |
| + | For example: |
| + | |
| + | H_0001->H_0001 HAPLO1 2332323244332 |
| + | H_0001->H_0001 HAPLO2 2332323422132 |
| + | H_0002->H_0002 HAPLO1 3332323244332 |
| + | H_0002->H_0002 HAPLO2 3311321242332 |
| + | ... |
| + | |
| + | HapMap format HapMap SNP File |
| + | ----------------------------- |
| + | legend file downloaded from HapMap website |
| + | |
| + | HapMap format HapMap Haplotype File |
| + | ----------------------------------- |
| + | phase file downloaded from HapMap website |
| + | |
| + | |
| | | |
| == Options == | | == Options == |