Started with data from: "Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake", Malinsky et al 2015. Downloaded VCF from http ...
I calculated pi diversity using both vcftools and pixy. The estimates from vcftools range from 0-0.0020 whereas the ones from pixy range from 0-0.4. Here is the pipleline I used to generate these.
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