Popgen: Difference between revisions
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In the resulting experiment's menu select "Analyze Diversity". | In the resulting experiment's menu select "Analyze Diversity". | ||
[[File:Screen_Shot_2016-02-09_at_11.14.11_AM.png| | [[File:Screen_Shot_2016-02-09_at_11.14.11_AM.png|400px|Diversity analysis menu option]] | ||
===3. Open the finished result=== | ===3. Open the finished result=== | ||
Revision as of 18:41, 9 February 2016
CoGe can generate basic population genetics summary statistics given a GVCF input file and an annotation genome.
Summary Statistics
Summary statistics 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 theta
- Tajima's D
Steps
1. Load a GVCF file
See the LoadExperiment tool to load a GCVF file against an existing genome in CoGe.
2. Analyze Diversity
In the resulting experiment's menu select "Analyze Diversity".
3. Open the finished result
Open the result in the PopGen tool to see results in tabular and graphical form.
