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Comparing complex variants in family trios

Berke Ç. Toptaş, Goran Rakocevic, Péter Kómár, Deniz Kural
doi: https://doi.org/10.1101/253492
Berke Ç. Toptaş
1Seven Bridges Genomics, 1 Main Street, Cambridge, MA 02142 USA
2SBGD Inc, 215 First Street, Cambridge MA 02142 USA
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Goran Rakocevic
1Seven Bridges Genomics, 1 Main Street, Cambridge, MA 02142 USA
2SBGD Inc, 215 First Street, Cambridge MA 02142 USA
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Péter Kómár
1Seven Bridges Genomics, 1 Main Street, Cambridge, MA 02142 USA
2SBGD Inc, 215 First Street, Cambridge MA 02142 USA
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Deniz Kural
1Seven Bridges Genomics, 1 Main Street, Cambridge, MA 02142 USA
2SBGD Inc, 215 First Street, Cambridge MA 02142 USA
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Abstract

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{at}hotmail.com

Supplementary information: Supplementary materials are available at Biorxiv.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 24, 2018.
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Comparing complex variants in family trios
Berke Ç. Toptaş, Goran Rakocevic, Péter Kómár, Deniz Kural
bioRxiv 253492; doi: https://doi.org/10.1101/253492
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Comparing complex variants in family trios
Berke Ç. Toptaş, Goran Rakocevic, Péter Kómár, Deniz Kural
bioRxiv 253492; doi: https://doi.org/10.1101/253492

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