550
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Reference Haplotype Set
: 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".
: 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
; --vcfReference
: This option specifies that the provided --refHaps file is provided in [http://www.1000genomes.org/wiki/Analysis/vcf4.0 VCF format] , no --refSNPs file needed.
: This option specifies that the provided --refHaps file is provided in [http://www.1000genomes.org/wiki/Analysis/vcf4.0 VCF format] , no --refSNPs file needed.
