RT Journal Article
SR Electronic
T1 Comparing complex variants in family trios
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 253492
DO 10.1101/253492
A1 Berke Ç. Toptaş
A1 Goran Rakocevic
A1 Péter Kómár
A1 Deniz Kural
YR 2018
UL http://biorxiv.org/content/early/2018/01/24/253492.abstract
AB 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.gitContact: cagkantoptas{at}hotmail.comSupplementary information: Supplementary materials are available at Biorxiv.