DHE calculation information from the Marchantia pangenome paper (https://doi.org/10.1038/s41588-024-02071-4)

This item contains scripts and datasets used to calculate Tajima's D, Fay and Wu's H and Zeng's E statistics on SNP data from Marchantia polymorpha (as well as on A. thaliana and M. truncatula). Folder M.polymorpha_file_processing contains scripts used to pre-process the SNP data, DHE_calculation_scripts contains the scripts to calculate D, H and E on unfolded SNP dataset (with ancestral allele known) and to calculate Tajima's D on the whole SNP dataset. The same calculations were also performed on M. truncatula and A. thaliana SNP data, downloaded at the links specified in the read_me_links file. The last folder contains vcf files of the outgroups used for the calculation on A. thaliana. Those VCFs were producted based on sequencing data from 30 A. halleri (PRJNA592307) and 29 A. lyrata (PRJNA357372), respectively mapped on the TAIR10 genome and for which polymorphic positions from the A. thaliana SNP dataset were called.