This repository contains the code for the RFMix-reader manuscript that
describes the RFMix-reader software.
Motivation: Local ancestry inference is a powerful technique in genetics,
revealing population history and the genetic basis of diseases. It is
particularly valuable for improving eQTL discovery and fine-mapping in admixed
populations. Despite the widespread use of the RFMix software for local
ancestry inference, large-scale genomic studies face challenges of high memory
consumption and processing times when handling RFMix output files.
Results: Here, I present RFMix-reader, a new Python-based parsing software,
designed to streamline the analysis of large-scale local ancestry datasets. This
software prioritizes computational efficiency and memory optimization, leveraging
GPUs when available for additional speed boosts. By overcoming these data
processing hurdles, RFMix-reader empowers researchers to unlock the full
potential of local ancestry data for understanding human health and health
disparities.
Availability: RFMix-reader is freely available on PyPI
at
https://pypi.org/project/rfmix-reader/,
implemented in Python 3, and supported on Linux, Windows, and Mac OS.
Contact: KynonJade.Benjamin@libd.org
Supplementary information: Supplementary data are available at
https://rfmix-reader.readthedocs.io/en/latest/.
Analysis-ready genotype data will be shared with researchers who obtain database of Genotypes and Phenotype (dbGaP) access (phs000979.v3.p2). The 1000 Genomes Project reference data are available at http://www.internationalgenome.org/data/. The simulated data used in the benchmarking analyses are available on Synapse syn61691659. The real data will be shared with researchers who obtain access to the genotype data (phs000979.v3.p2) upon request. All scripts generated in this paper are available through GitHub at https://github.com/heart-gen/rfmix_reader-benchmarking.
This work was supported by grants from the National Institutes of Health, National Institute on Minority Health and Health Disparities (NIMHD) K99MD016964.
If you the RFMix-reader software or anything in this repository please cite the
following pre-print: https://doi.org/10.1101/2024.07.13.603370.
Kynon JM Benjamin. "RFMix-reader: Accelerated reading and processing for local ancestry studies." bioRxiv. 2024. DOI: 10.1101/2024.07.13.603370.
This license lets others remix, tweak, and build upon our work non-commercially as long as they acknowledge our work.