avg_pi was bigger than that of vcftools

[feiyu007]

Describe the problem you are having
A clear and concise description of what problem you are encountering. Note: the intent of these issues are to report problems with pixy usage/installation. We cannot advise on the biological interpretation of results generated by pixy.

A reproducible example of the problem
If your question is about how your dataset is specifically being processed by pixy, please copy and paste the following:
(1) The command you used to run pixy, including all arguments
(2) A subset of your VCF and the full populations file
(3) Any other files needed to reproduce the problem (sites, bed file, etc.)

[ksamuk]

Hi there, I'd like to help you but you didn't follow the instructions for posting an issue. Please read the text of your issue, which contains those instructions.