Abstract
BackgroundHaloplex 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.ResultsWe 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.ConclusionspyAmpli 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.
Highlights
Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels
Low-cost targeted resequencing using specific gene panels in large sample cohorts is widely used in diagnostic settings and forms the current gold standard for multiple reasons
The default somatic mode of pyAmpli requires an amplicon-design file provided by the manufacturer, a paired tumor-normal variant calling file (VCF) and a normal and tumor alignment file (BAM) as input
Summary
Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. We present pyAmpli, a platform independent parallelized Python package that leverages amplicon specific information during variant filtering. PyAmpli can be applied in an oncological setting, after somatic tumor-normal variant calling as well in germline disease-gene screening projects.
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