Welcome to rfmix-reader’s documentation!

rfmix-reader gives fast, memory-light access to local-ancestry output — RFMix (.msp.tsv, .fb.tsv), FLARE and haptools simulations — as one lazily-evaluated xarray.Dataset backed by a per-chromosome Zarr cache: one streaming pass over the source, then instant reopen, with position queries, BED intervals, Parquet export, interpolation and gnomix-style phasing on the same object.

Table of Contents

• Install
  • Extras
  • LoGicAl (R side)
  • GPU acceleration
  • Development
• Usage
  • Opening data
  • The Dataset
  • Operations
  • Phasing
  • Ancestry-specific allele frequencies (LoGicAl)
  • Haptools simulations
  • Visualization
  • Migrating from 0.x
• API Reference
  • Readers and cache
  • The Dataset
  • Operations
  • Phasing and imputation
  • Formats
  • Visualisation
  • Reference panels, backends, command line

Citation

If using, please cite the following pre-print:

Kynon JM Benjamin. “RFMix-reader: Accelerated reading and processing for local ancestry studies.” bioRxiv. 2024. DOI: 10.1101/2024.07.13.603370

Comments and bugs

You can get the source code and open issues on Github.

Indices and tables

• Index

• Search Page