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; --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.
; --rs
: In combination with --vcfReference, allows to use rs GWAS SNP identifiers
== Model Refinement ==
== Model Refinement ==
