Learned a new bioinformatics trick today while using VCFtools to analyze nucleotide diversity for the Amazon molly (Poecilia formosa), an intriguing asexually reproducing (gynogenesis) fish. To calculate withing species/population Pi from a big vcf file containing multiple populations, provide a list containing all the individuals’ names from one population in a file (e.g., LIST), and use the following command “vcftools –vcf input.vcf –keep LIST –site-pi –out LIST_Pi”. Thanks to popgencode!
