Code used in genomic analyses of hunter-gatherer populations by Christina Bergey (website) et al. A paper describing the method been submitted for publication and is available as a preprint from bioRxiv:
Bergey CM, Lopez M, Harrison GF, Patin E, Cohen J, Quintana-Murci L, Barreiro LB, & Perry GH. (Preprint). Polygenic adaptation and convergent evolution across both growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers.
The steps of the pipeline are controlled with the Snakemake file, Snakefile.