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Comparing complex variants in family trios

By Berke Ç. Toptaş, Goran Rakocevic, Péter Kómár, Deniz Kural

Posted 24 Jan 2018
bioRxiv DOI: 10.1101/253492 (published DOI: 10.1093/bioinformatics/bty443)

Motivation: Several tools exist to count Mendelian violations in family trios by comparing variants at the same genomic positions. This naive variant comparison however, fails to assess regions where multiple variants need to be examined together, resulting in reduced accuracy of existing Mendelian violation checking tools. Results: We introduce VBT, a trio concordance analysis tool, that identifies Mendelian violations by approximately solving the 3-way variant matching problem to resolve variant representation differences in family trios. We show that VBT outperforms previous trio comparison methods by accuracy. Availability: VBT is implemented in C++ and source code is available under GNU GPLv3 license at the following URL: https://github.com/sbg/VBT-TrioAnalysis.git Contact: cagkantoptas@hotmail.com Supplementary information: Supplementary materials are available at Biorxiv.

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