kkorunes/CaboVerde_Demographic_Analyses

Scripts for analyzing population history in Cabo Verde # CaboVerde_Demographic_Analyses This repository contains scripts for analyzing population history in Cabo Verde. The following analyses were performed in the Goldberg Lab at Duke University by Katharine Korunes (contact: kkorunes@gmail.com). ## Citation Our associated preprint, *"Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans,"* is available here: biorxiv.org ## Datasets - 1000 Genomes resequencing data can be accessed here: internationalgenome.org - Cabo Verdean data originally described in Beleza et al. 2013 does not allow for public release of genotype data; however, inferred local ancestry information used in this study can be found at doi.org ## Software and scripts from external sources - plink v1.9 cog-genomics.org - ADMIXTURE v1.3.0 dalexander.github.io - SHAPEIT v2 mathgen.stats.ox.ac.uk - RFMix v1.5.4 sites.google.com - EIGENSOFT v3 ***convertf*** github.com - ALDER v1.03 cb.csail.mit.edu - MULTIWAVER v2.0 picb.ac.cn - LAD-based Zaitlen et al. method github.com - ANCESTOR github.com - Ancestry specific IBD Ne faculty.washington.edu - RefinedIBD faculty.washington.edu - Kinship method from Ochoa & Storey 2019 (doi: dx.doi.org) github.com - Cytoscape v3.8 cytoscape.org - GARLIC v1.1.6 github.com - R v3.6.1 r-project.org ## The 3 directories here contain code f …