This repository contains the source code for the publication titled "Reconstruction of private genomes through reference-based genotype imputation" by Matthew J. Mosca and Hyunghoon Cho in Genome Biology. Due to the sensitive nature of our investigation, we have made the repository access-controlled. We will share access to our code with anyone affiliated with an academic or research organization who provides a valid rationale for needing access. We consider valid rationale to include use for ethical academic research purposes and to specifically not include use against public imputation servers. If you would like access, please provide (1) your affiliation, (2) a brief description of the purposes for which you are requesting access, and (3) a statement affirming that you will use the code only for research purposes and will not use it against existing imputation servers or attempt to reconstruct data to which you do not have direct access. We expect to be able to approve requests for access within 2–3 weeks. If you have been given access, please see the included README for an explanation of our code.