Popgen

CoGe can generate basic 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. In the resulting experiment's menu select "Analyze Diversity". 3. Open the finished result in the PopGen tool to see results in tabular and graphical form.