Scripts, data, and figures for forward evolutionary simulations from Zhang et al. manuscript.

The r06.1 directories contain the simulations included in the paper. These apply a stabilizing selection fitness model and measure LD as well as snp-pair effect correlation. Scripts adapted from an early implementation credited to Arun Durvasula. Details of this are in the scripts and notebook directories.

I used Corbin Quick's emeraLD software to compute LD. I am using a custom build of that includes a bugfix and the ability to receive a list of SNPs to interrogate.

Zhang et al. (2023). Pervasive correlations between causal disease effects of proximal SNPs vary with functional annotations and implicate stabilizing selection. In medRxiv (p. 2023.12.04.23299391). https://doi.org/10.1101/2023.12.04.23299391