This is the repository that contains code used in the paper "Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals" by Kustin et al. https://www.medrxiv.org/content/10.1101/2021.04.06.21254882v2
Input files for this code ("frequency files") can be created by the AccuNGS pipeline: https://github.com/SternLabTAU/AccuNGS.