VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants.
Customizable ranking
Genomic annotation
Next-generation sequencing
Pathogenicity predictions
Variant prioritization
Journal
Genomics, proteomics & bioinformatics
ISSN: 2210-3244
Titre abrégé: Genomics Proteomics Bioinformatics
Pays: China
ID NLM: 101197608
Informations de publication
Date de publication:
10 2019
10 2019
Historique:
received:
20
11
2018
revised:
26
08
2019
accepted:
08
11
2019
pubmed:
26
11
2019
medline:
14
4
2020
entrez:
26
11
2019
Statut:
ppublish
Résumé
Next-generation sequencing (NGS) technologies generate thousands to millions of genetic variants per sample. Identification of potential disease-causal variants is labor intensive as it relies on filtering using various annotation metrics and consideration of multiple pathogenicity prediction scores. We have developed VPOT (variant prioritization ordering tool), a python-based command line tool that allows researchers to create a single fully customizable pathogenicity ranking score from any number of annotation values, each with a user-defined weighting. The use of VPOT can be informative when analyzing entire cohorts, as variants in a cohort can be prioritized. VPOT also provides additional functions to allow variant filtering based on a candidate gene list or by affected status in a family pedigree. VPOT outperforms similar tools in terms of efficacy, flexibility, scalability, and computational performance. VPOT is freely available for public use at GitHub (https://github.com/VCCRI/VPOT/). Documentation for installation along with a user tutorial, a default parameter file, and test data are provided.
Identifiants
pubmed: 31765830
pii: S1672-0229(19)30149-4
doi: 10.1016/j.gpb.2019.11.001
pmc: PMC7056850
pii:
doi:
Substances chimiques
3-Hydroxyanthranilate 3,4-Dioxygenase
EC 1.13.11.6
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
540-545Informations de copyright
Copyright © 2019 The Authors. Published by Elsevier B.V. All rights reserved.
Références
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Genome Res. 2005 Aug;15(8):1034-50
pubmed: 16024819
PeerJ. 2015 Mar 03;3:e796
pubmed: 25780760
Nature. 2016 Aug 17;536(7616):285-91
pubmed: 27535533
BMC Bioinformatics. 2017 Jul 17;18(1):341
pubmed: 28716001
Hum Mol Genet. 2015 Apr 15;24(8):2125-37
pubmed: 25552646
Nat Methods. 2010 Apr;7(4):248-9
pubmed: 20354512
Circ Genom Precis Med. 2018 Mar;11(3):e001978
pubmed: 29555671
Nature. 2013 Jan 10;493(7431):216-20
pubmed: 23201682
Hum Mutat. 2013 Jan;34(1):57-65
pubmed: 23033316
PLoS Comput Biol. 2010 Dec 02;6(12):e1001025
pubmed: 21152010
N Engl J Med. 2017 Aug 10;377(6):544-552
pubmed: 28792876
Genet Med. 2019 May;21(5):1111-1120
pubmed: 30293987
Genome Res. 2009 Sep;19(9):1553-61
pubmed: 19602639
Nucleic Acids Res. 2010 Sep;38(16):e164
pubmed: 20601685
Discov Med. 2011 Jul;12(62):41-55
pubmed: 21794208
Nat Genet. 2014 Mar;46(3):310-5
pubmed: 24487276
Nucleic Acids Res. 2011 Sep 1;39(17):e118
pubmed: 21727090
Nat Methods. 2014 Apr;11(4):361-2
pubmed: 24681721
Nat Genet. 2016 Dec;48(12):1581-1586
pubmed: 27776117
Nat Protoc. 2009;4(7):1073-81
pubmed: 19561590