analyses of experimentally and naturally infected prairie dogs to determine genetic basis of resistance
This repository will contain the pipeline, an R script used to run OutFLANK, and any other code necessary to replicate the analyses.
The analyses outlined here assume that we are starting with a quality-filtered vcf file, e.g., such as one generated in https://github.com/CassinSackett/SNP_capture/blob/master/pipeline.md