What it does

Calculates heterozygosity and Fst for loci in data from the Human Genome Diversity Project (HGDP).

The Count tool combines data from HGDP_FinalReport_Forward.txt and HGDP_Map.txt (both of which are available from http://www.hagsc.org/hgdp/files.html). This information is filtered for two sets of individuals to represent two populations which are defined in the input for this Count tool.

The output of the Count tool is a file containing the following columns:

1. Name of the marker
2. Chromosome position
3. Major Allele in the first population frequency of the major allele
4. Number of Individuals in the first population
5. Expected Heterozygosity in the first population
6. Observed Heterozygosity in the first population
7. Major Allele in the second Population
8. Frequency of the Major Allele, Number of Individuals in the second population
9. Expected Heterozygosity in the second population
10. Observed Heterozygosity in the second population
11. Fst between the two populations

This output is used as input for the SmileFinder tool.

Please note that the markers must be sorted in order according to their chromosome and position in order for SmileFinder to work properly.

If you wish to create your own input file for SmileFinder without using Count, the fields required are:

1. Name of the marker
2. Chromosome
3. Position
4. Observed Heterozygosity in both populations
5. Fst

The other fields are not required and can be left empty.

As noted above, your markers must be sorted in order according to their chromosome and position prior to your data being analysed by SmileFinder.