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.