konradjk / gnomad_high_ad_hets

gnomAD high allele balance error mode

This repo contains code for the analysis and figures in our recent preprint that identifies an error mode in gnomAD relating to individuals with high allele balance (fraction of alternate reads) being called as heterozygotes.

Analysis code

find_high_ad_hets.py requires Hail 0.2, and only the first section (--find_high_ad_hets) can be run without access to the restricted individual-level dataset.

The remainder of the analysis code is provided as-is for reference.

Plotting code

plot_high_ad_het_data.R includes the code to parse, process, and plot the resulting data, in order to create the 3 figures in the manuscript.