SDS_Drivers

Code for Ming and Harpak, 2026. "Drivers of systemic male-female allele frequency divergence in humans"

Data

Data for each biobank was obtained from their respective platforms

gnomAD

VCF files from gnomAD v3 are freely available on the gnomAD website https://gnomad.broadinstitute.org/data#v3

UK Biobank

Data was collected on the UKB Research Analysis Platform (UKBRAP). Sample and initial SNP filtering was performed on the platform directly.

Pipelines for generating VCF files were performed using plink via the swiss army knife tool in the dx command line environment.

All of Us

Data was collected on the AoU Researcher Workbench. As with UKB, sample and SNP filtering was performed on the workbench.

Pipelines for generating VCF files were performed using python via jupyter notebooks on the workbench.

Code

1. AnalyzeCounts_NewMethod_MAGMAsnps_slurm.R: the primary analysis file for generating chi-sq p-values and Hardy Weinberg Equilibrium p-values, as well as generating associated figures. The .slurm file is code to run this on computing cluster
2. Expression Heatmaps.R: Code for analyzing expression of genes in testes.
3. GIM_GeneConcordance_Code.R: Code for comparing sperm-expressed genes with Bhutani et al. results.