RFMix-reader: Accelerated reading and processing for local ancestry studies
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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 eiciency 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/ .
