I am trying to add a standard desviation to the pi values obtained from SNPgenie ( https://github.com/chasewnelson/SNPGenie#output ) I checked that I can add a bootstrap value if I use the type of analysis WITHIN-GROUP ANALYSIS and BETWEEN-GROUP ANALYSIS but no for WITHIN-POOL ANALYSIS, this is the type of analysis that I am doing for get the diversity value (pi value) of my NGS vcf files.

So, is there another way to get a standard desviation of my pi values?

Thanks in advantage.