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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 ==
