Authors: Sarah Perkins, Daniel Neafsey, Angela Early
Scripts to run DFE-alpha in jackknife iteration. Includes some primary data files and config files. DFE-executables and reference data must be downloaded and recomputed from source. https://sourceforge.net/projects/dfe-alpha-k-e-w/
Scripts to calculate divergence statistics from PlasmoDB datasets (https://plasmodb.org/plasmo/app). Includes some manual steps via PlasmoDB GUI search functions. These steps are described in corresponding files.
Scripts to calculate diversity statistics from MalariaGEN Pf7 datasets after VCF filtering. Pf7 release downloads are described here: https://www.malariagen.net/data_package/open-dataset-plasmodium-falciparum-v70/
Scripts for selecting gene sets and breadth labels from Malaria Cell Atlas P. falciparum SS2 set1, as downloaded from: https://www.malariacellatlas.org/data-sets/
Scripts for downloading and filtering Pf7 VCFs to include chosen population samples and variants passing QC and variant type fitlers.
Script to select specific samples from Pf7 metadata. Includes selection step to isolate clonal clusters from hmmIBD output.
Includes input and output data needed for or produced by scripts in all other directories, including some intermediate files.