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; --refHaps [filename]
; --refHaps [filename]
: This option specifies the name of a text file listing reference haplotypes. This file is typically generated by [[MaCH]].
: This option specifies the name of a text file listing reference haplotypes. This file is typically generated by [[MaCH]].
: Each line in the reference haplotype file starts with a haplotype label. This is followed by a series of alleles (one character per marker), optionally separated by whitespace to improve readability. Acceptable allele labels are "A", "C", "G", "T"; upper and lower case letters are treated identically. The digits "1", "2", "3", "4" are also acceptable and treated as aliases for "A", "C", "G", "T".
: Each line in the reference haplotype file starts with a haplotype label. This is followed by a series of alleles (one character per marker), optionally separated by whitespace to improve readability. Acceptable allele labels are "A", "C", "G", "T","I","D","R" (I..Insertions, D..Deletion, R..Reference); upper and lower case letters are treated identically. The digits "1", "2", "3", "4" are also acceptable and treated as aliases for "A", "C", "G", "T".
; --vcf
: This option specifies that the provided --refHaps file is saved in the [http://www.1000genomes.org/wiki/Analysis/vcf4.0 VCF format] - no --refSNPs file needed.
; --snpAliases [filename]
; --snpAliases [filename]
