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.
