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pyAmpli

Tijdschriftbijdrage - e-publicatie

Ondertitel:an amplicon-based variant filter pipeline for targeted resequencing data
Background: Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in subsequent data-analysis. No variant filtering rationale addressing amplicon enrichment related systematic errors, in the form of an all-in-one package, exists to our knowledge. Results: We present pyAmpli, a platform independent parallelized Python package that implements an amplicon-based germline and somatic variant filtering strategy for Haloplex data. pyAmpli can filter variants for systematic errors by user pre-defined criteria. We show that pyAmpli significantly increases specificity, without reducing sensitivity, essential for reporting true positive clinical relevant mutations in gene panel data. Conclusions: pyAmpli is an easy-to-use software tool which increases the true positive variant call rate in targeted resequencing data. It specifically reduces errors related to PCR-based enrichment of targeted regions.
Tijdschrift: BMC bioinformatics
ISSN: 1471-2105
Volume: 18
Jaar van publicatie:2017
Trefwoorden:A1 Journal article
BOF-keylabel:ja
BOF-publication weight:3
CSS-citation score:1
Authors from:Higher Education
Toegankelijkheid:Open