THORIN v1.2 : Target Haplotype ORigin INference

THORIN is a tool for mapping Identify-By-Descent (IBD) and inferring the Parent-of-Origin of alleles.

What's new in v1.2?:

THORIN v1.2 uses the same algorithm as in THORIN v1.1, but offers the opportunity to

• write the ouptut in a vcf.gz or bcf format (add the suffix vcf.gz/bcf to the output file)
• output IBD segments (option --ibd)
• output an IBD-based scaffold VCF/BCF file that allows re-estimation of haplotype to perform inter-chromosomal phasing (option --scaffold)

Citation

If you use THORIN in your research work, please cite the following papers:

Hofmeister, R.J. et al. Parent-of-Origin inference for biobanks. Nature Communication 2022. https://doi.org/10.1038/s41467-022-34383-6

Hofmeister, R.J. et al. Parent-of-origin effects on complex traits in up to 236,781 individuals. Nature 2025. https://doi.org/10.1038/s41586-025-09357-5

Documentation

Documentation, installation instructions and tutorials can be found at:

https://rjhfmstr.github.io/THORIN/

License

This project is licensed under the MIT License - see the LICENSE file for details