This repo contains code for "Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae".
The main simulation used can be found at simulation/scripts/spatial_sweep.slim; functions for processing tree sequences and calculating per-variant frequency and area can be found in simulation/scripts/frequency_area.py.
Spatial genome scans on Anopheles gambiae data were carried out using anopheles/scripts/anopheles_SNP_genome_scan.py and analyzed using anopheles/anopheles-analysis.Rmd.
The entire analysis can be visualized and browsed here, including an interactive frequency-area plot of genome-wide WSF outliers and searchable table of all SF outliers identified in our analysis.