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===2. Analyze Diversity=== | ===2. Analyze Diversity=== | ||
Once the GVCF experiment is loaded, navigate to the experiment view and select "Analyze Diversity". | |||
[[File:Screen_Shot_2016-02-09_at_11.14.11_AM.png|400px|Diversity analysis menu option]] | [[File:Screen_Shot_2016-02-09_at_11.14.11_AM.png|400px|Diversity analysis menu option]] | ||
Revision as of 17:54, 1 March 2016
CoGe can generate basic population genetics summary statistics given a GVCF input file and an annotated genome.
Summary Statistics
These summary statistics are computed per feature overall (gene, CDS, etc) and by 0/4-fold degeneracy (for CDS only):
- Nucleotide diversity (pi) - average number of pairwise differences between variant sequences
- Watterson's estimator (theta)
- Tajima's D
Steps
1. Load a GVCF file
See the LoadExperiment tool for loading a GCVF file against an existing genome in CoGe.
2. Analyze Diversity
Once the GVCF experiment is loaded, navigate to the experiment view and select "Analyze Diversity".
3. Open the finished result
Open the result in the PopGen tool to see results in tabular and graphical form.
