Data from Gunnarsson et al. bioRxiv, 2024

This page is under contruction and will contain data related to the paper:

A scalable approach for genome-wide inference of ancestral recombination graphs. Á. Gunnarsson, J. Zhu, B. Zhang, Z. Tsangalidou, A. Allmont, P. Palamara. bioRxiv. September 2024. [preprint]

Example Data

A small example dataset for running the threads package can be downloaded from example.zip. This dataset aligns with the usage instructions in the manual.

The archive contains the following files:

example/
├── example_data.bim
├── example_data.fam
├── example_data.map
├── example_data.pgen
├── Ne10000.demo
└── wgs.map.gz

1,000 Genomes Project ARGs

These folders contain ARGs used for the imputation experiments described in the paper.

  • The EUR folder contains .threads and .argn ARGs for 2,251 unrelated 1000 Genomes Project samples, excluding 10 randomly selected EUR genomes held out for imputation.
  • The AFR folder contains .threads and .argn ARGs for the same 2,254 samples, excluding 7 randomly selected AFR genomes held out for imputation.

Each folder also includes:

  • impute{EUR,AFR}.heldout_samples.txt: a list of individual IDs held out for imputation
  • impute{EUR,AFR}.panel.fam: a list of individual IDs used as the imputation panel and included in the ARGs