Tagging Output Options
-pairwiseTagging
Generates pairwise tagging information in <inputfile>.TAGS and .TESTS
-aggressiveTagging
As above but generates 2-marker haplotype tags unless specified otherwise by -aggressiveNumMarkers
-tagrsqcounts
Generates conditional haplotype probabilities from tagger in <inputfile>.CHAPS
-aggressiveNumMarkers <2,3>
Specifies whether to use 2-marker haplotype tags or 2 and 3-marker haplotype tags.
-maxNumTags <n>
Only selects <n> best tags.
-includeTags <markers>
Forces in a comma separated list of marker names as tags.
-includeTagsFile <file>
Forces in a file (or http:// location) of one marker name per line as tags.
-excludeTags <markers>
Excludes a comma separated list of marker names from being used as tags.
-excludeTagsFile <file>
Excludes a file (or http:// location) of one marker name per line from being used as tags.
-captureAlleles <file>
Capture only the alleles contained in a file (or http:// location) of one marker name per line.
-designScores <file>
Specify design scores in a file (or http:// location) of one marker name and one score per line.
-mindesignscore <threshold>
Specify a minimum design score threshold.
-mintagdistance <distance>
Specify a minimum distance in bases between picked tags.
-taglodcutoff <thresh>
Tagger LOD cutoff for creating multimarker tag haplotypes.
-tagrsqcutoff <thresh>
Tagger r^2 cutoff.