ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 11 2019
01 11 2019
Historique:
received:
10
03
2019
revised:
26
04
2019
accepted:
23
05
2019
pubmed:
28
5
2019
medline:
2
7
2020
entrez:
29
5
2019
Statut:
ppublish
Résumé
We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 31134279
pii: 5499079
doi: 10.1093/bioinformatics/btz431
pmc: PMC6853681
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4754-4756Subventions
Organisme : Medical Research Council
ID : MR/S006753/1
Pays : United Kingdom
Informations de copyright
© The Author(s) 2019. Published by Oxford University Press.
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