Archive Meta Data

Author(s)

Leonardo Cobuccio, Kirstine Ravn, Simon Rasmussen

Title

Simulated and real ancient genomes analyzed by HAPI to identify the CCR5delta32 deletion

Description

Simulated and real ancient genomes on which the model HAPI (Haplotype-Aware Probabilistic model for Indels) was developed to identify the CCR5delta32 deletion, appearing in the pre-print "Tracing the evolutionary path of the CCR5delta32 deletion via ancient and modern genomes" https://doi.org/10.1101/2023.06.15.23290026

This archive contains:

Simulated samples: aDNA_simulated_paper.zip
- 144 ancient simulated genomes aligned to the references GRCh37 and Collapsed
- GRCh37 and Collapsed genomic references in .fa format
- list of samples to run HAPI
- list of the 4 SNPs in high LD with the deletion
- folder results with the results of running HAPI on all of the samples with the default settings

The real ancient samples are in the file aDNA_real_paper.zip and contain:
- 135 neolithic samples aligned to the references GRCh37 and Collapsed
- 31 bronze age samples aligned to the references GRCh37 and Collapsed
- 47 Botai samples aligned to the references GRCh37 and Collapsed
- 252 viking samples aligned to the references GRCh37 and Collapsed

All the alignments are in cram format.

For more details on how the data was simulated and the origin of the ancient samples, please refer to the preprint.

The software is available as a pypi package at https://pypi.org/project/hapi-pyth/ and instructions on how to run it are available at https://github.com/RasmussenLab/HAPI/tree/main