Each analysis has its own folder along with README.md that includes env needed, input/ output data and general description.
- admixture - Instruction to running ADMIXTURE
- docs/malaria_f2m.md - Guide to create GenomicsDB and filtering for Plasmodium species
- moi - Calculation of Fws from filtered merged VCF
- ibd - Calculation of indentity by descent with hmmIBD from binary matrix based on Ernest's scripts
- pca - Example of PCA with PLINK plus visualisation
- selection - Calculation of selection metrics with rehh package from binary matrix based on Ernest's scripts
- utils - helper functions used across the scripts
Please share bugs, incosistencies, ideas over an e-mail