/mcps_ibd_freq_calc

Compute relatedness corrected allele frequencies using IBD segments

Primary LanguagePython

This repository contains scripts and code to compute ancestry-specific allele frequencies from Ziyatdinov, A., Torres, J., Alegre-Diaz, J. et a. (2022). Genotyping, sequencing and analysis of 140,000 adults from the Mexico City Prospective Study. bioRxiv, 2022-06. https://doi.org/10.1101/2022.06.26.495014

The scripts in mcps-rfmix-processing extrapolate local ancestry estimates from RFMix run on array variants to WES/WGS sites.

The program in calc-ibd-freq uses these estimates to compute raw and relatedness corrected allele frequencies.

Contact

  • Tyler Joseph: tyler.joseph at regeneron dot com
  • Andrey Ziyatdinov: andrey.ziyatdinov at regeneron dot com