Code relating to the Bamako WGS population genomics analysis as published in the following paper:
Love, R. R., Steele, A. M., Coulibaly, M. B., Traore, S. F., Emrich, S. J., Fontaine, M. C. and Besansky, N. J. (2016), Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing. Mol Ecol, 25: 5889–5906. doi:10.1111/mec.13888
This repository contains the Python script, vcf-consensus.py, used to generate reference sequences from each pool, and contains an R script corresponding to 3 of the 4 main figures as well as a supplementary figure.