TRIBES

TRIBES is a user-friendly platform for relatedness detection in genomic data. TRIBES is the first tool which is both accurate (up to 7th degree) and combines essential data processing steps in a single platform.

Accurately classifying the degree of relatedness between pairs of individuals has multiple important applications, including disease gene discovery, removal of confounding relatives in genome wide association studies (GWAS) and family planning. Currently no tools are available which are accurate beyond 3rd degree and combine the necessary data processing steps for accuracy and ease of use. To address this we have developed ‘TRIBES’, a user-friendly platform which leverages the GERMLINE algorithm to accurately identify distant relatives. TRIBES enables user-guided data pruning, phasing of genomes, IBD segment recovery, masking of artefactual IBD segments and finally relationship estimation. To facilitate ease-of-use we employ ‘Snakemake’, a workflow tool which enables flexibility and reproducibility.

We demonstrate the accuracy of TRIBES in our publications [here](https://www.biorxiv.org/content/10.1101/686253v1) and [here](https://www.biorxiv.org/content/10.1101/685925v2)

Briefly, input data to TRIBES is quality control filtered, joint sample VCF. TRIBES then follows these steps:

  1. The VCF is filtered using quality metrics contained within the VCF file.
  2. The resultant VCF is then phased using BEAGLE.
  3. IBD Segments are then estimated using GERMLINE.
  4. Artefactual IBD is masked using a reference file by adjusting segment endpoints.
  5. Adjusted IBD Segments are then summed to estimate relationships.
  6. TRIBES returns result files, including .csv of estimated relationships.

The full TRIBES pipeline is described in detail in [Supplementary Material](https://www.biorxiv.org/content/10.1101/686253v1.supplementary-material).

Watch a short video introducing TRIBES and its applications

_images/tribes_video.jpg

Contact

Please report any issues or ideas at: https://github.com/aehrc/TRIBES/issues

Or contact the TRIBES team at: TBP

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