ArticleBioinformatics (Oxford, England)2018
Comparing complex variants in family trios.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance.Genome biology · 2023Article
- E-Pedigrees: a large-scale automatic family pedigree prediction application.Bioinformatics (Oxford, England) · 2021Article
- Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.Nature biotechnology · 2021Article
- Best practices for variant calling in clinical sequencing.Genome medicine · 2020Review
- Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance.Frontiers in genetics · 2020Review
- An open resource for accurately benchmarking small variant and reference calls.Nature biotechnology · 2019Article
- geck: trio-based comparative benchmarking of variant calls.Bioinformatics (Oxford, England) · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
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, which 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 and implementation: 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. Supplementary information: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.