Simulation examples to test github.com/sdtemple/isweep workflows

This dataset includes some small VCF and tree sequence data to test the github.com/sdtemple/isweep workflows. The README.md provides detailed instructions and commands. Scripts are provided that document how the small data was simulated, and commands to start the workflows. The simulated data examples are:

10 autosomes of 100 cM for a staged exponential growth scenario

10 autosomes of 100 cM for a tetraploidy example with constant 10k Ne

American admixture from stdpopsim (100 AFR, 100 ASIA, 100 EUR, 50 ADMIX)

You should tar -xzvf the compressed folder. The resulting folder wilth be called "zenododata" after you decompress the tar ball. You will need to adjust some local file paths to run the workflows. The data is ready to run the workflows already, but you can re-generate data with the scripts if you want.

Note: I renamed "git mv" the "workflow/prepare" folder to "workflow/phasing-ancestry", so all terminal commands should be modified accordingly.

Note: I changed "ALPHA" in region of interest files to "INTERVALCOVERAGE" in revised workflows. You should go into the "dummy.roi.tsv" files and change "ALPHA" to "INTERVALCOVERAGE" in the header. Otherwise, you will get a Snakemake error.