Wow, Iverson's interview with McNeely gives an in-depth feel for the jazz scene in Champaign-Urbana in the early 1970s -- super interesting. As a jazz enthusiast and fan of the early to mid 1970s period, and someone who moved to C-U in 2015, that was fascinating!

The populations VCF import function is designed only for variant sites. You could re-export the VCF from populations with the alt population map. If you want to keep your filtering, you can use the loci that were not filtered by vcftools to make a whitelist to feed into populations at the same time

Yes, there is a flag to output all sites in the VCF file. The populations program will also calculate Pi and Dxy, accounting for variant/invariant sites, by default.

This project was led and implemented by Gio Madrigal (first, first author!) with assistance from Bushra Minhas.

The tool has two modes of operation – you can give it one or more queries, and it will k-merize and search for them in an assembly and the raw reads, or you can turn it loose to scan a long-read genome (and its raw reads) for inconsistent areas of assembly.

We built Klumpy – a combined k-mer search and visualization tool, written in Python – to help us find and verify antifreeze genes in fishes and we have since used it for a lot more.