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Revision as of 07:43, 19 September 2011
, 07:43, 19 September 2011→Target Haplotype Set
; --haps [filename]
; --haps [filename]
: This option specifies the name of a text file listing reference haplotypes. This file is typically generated by [[MaCH]]. The file should be formatted just like the reference haplotype file, described in the previous section.
: This option specifies the name of a text file listing reference haplotypes. This file is typically generated by [[MaCH]]. The file should be formatted just like the reference haplotype file, described in the previous section.
; --alias [filename]
: This option points to a file listing mappings between alternate marker names. Each row should include two columns. The first column lists a previous commonly used name for a marker (perhaps from an earlier version of dbSNP) and the second column lists the current preferred name for the marker. An example input file, which maps ids from the 1000 Genomes Project and earlier versions of dbSNP to build 134, see [http://www.sph.umich.edu/csg/abecasis/downloads/dbsnp134-merges.txt.gz dbsnp134-merges.txt.gz].
== Model Refinement ==
== Model Refinement ==
