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MaximumTaxaDiversity
MaximumTaxaDiversity identifies a subset of samples that will try to maximize heterozygosity of a marker set. Useful for selecting samples for marker validation to increase representation of heterozygous genotype calls.
Jar path:
to be added
Usage:
<No. of target markers> <Population size> <Min. heterozygous frequency> <Input HapMap file> <Output text file>
| Parameters | Description |
|---|---|
| Number of target markers (integer) | number of markers to select |
| Popoulation size (integer) | number of solutions to consider at a time (better results when higher but uses more RAM) |
| Minimum heterozygous frequency (decimal, 0 to 1) | minimum proportion of heterozygous samples for each marker. Higher value will result to higher likelihood of heterozygous calls. |
| Input hmp.txt (file) | hapmap file where to pick markers from |
| Output file (file) | output file, e.g. out.txt |
| Results and outputs | Description |
|---|---|
| Score | number of markers that passes (>=) the indicated minimum heterozygous percentage threshold |
| Text file | contains some information on the selected markers |
| Hapmap file | subset of the input hapmap file containing the selected markers only |
Updated