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Analysis scripts used in the academic manuscript accompanying the pixy software.

See the preprint here: https://www.biorxiv.org/content/10.1101/2020.06.27.175091v1

See the manuscript here: https://doi.org/10.1111/1755-0998.13326

Project Structure

  • The top level directory contains the R scripts (and Rstudio project file) used to generate the figures and analyses presented in the paper.
  • The 'data_generation' folder contains subfolders for each method used to:
    • Simulate sequence data using msprime
    • Call variants (i.e. create an all-sites VCF) from a subset of the the Ag1000g data.
    • Estimate pi, dxy, Watterson's theta, and Tajima's D from the simulated & Ag1000g datasets using a variety of methods, including pixy.