ArticleScientific reports2017
BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.Cell reports · 2025Article
- Novel microsatellite instability test of sebaceous tumours to facilitate low-cost universal screening for Lynch syndrome.Clinical and experimental dermatology · 2025Article
- Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time.Nucleic acids research · 2025Article
- Detection and variant characterization of lumpy skin disease virus from dairy cattle in India.Virus evolution · 2025Article
- Whole-genome sequencing surveillance of Siberian tick-borne encephalitis virus (TBEV) identifies an additional lineage in Kyrgyzstan.Virus research · 2025Article
- Rare variation in non-coding regions with evolutionary signatures contributes to autism spectrum disorder risk.Cell genomics · 2024Article
- SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection.Genome medicine · 2024Article
- UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example.BMC genomics · 2024Article
- Cell lineage analysis with somatic mutations reveals late divergence of neuronal cell types and cortical areas in human cerebral cortex.bioRxiv : the preprint server for biology · 2023Article
- The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection.Genome biology · 2023Article
- Targeted Whole Genome Sequencing (TWG-Seq) of Cucumber Green Mottle Mosaic Virus Using Tiled Amplicon Multiplex PCR and Nanopore Sequencing.Plants (Basel, Switzerland) · 2022Article
- Polygenic risk scores indicate extreme ages at onset of breast cancer in female BRCA1/2 pathogenic variant carriers.BMC cancer · 2022Article
- Clonal Hematopoiesis-Associated Gene Mutations in a Clinical Cohort of 448 Patients With Ovarian Cancer.Journal of the National Cancer Institute · 2022Article
- SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2021Article
- MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations.BMC medical genomics · 2021Article
- Development and Analytical Validation of a Targeted Next-Generation Sequencing Panel to Detect Actionable Mutations for Targeted Therapy.OncoTargets and therapy · 2021Article
- Determination of the phylogenetic origins of the Árpád Dynasty based on Y chromosome sequencing of Béla the Third.European journal of human genetics : EJHG · 2021Article
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5 authors.
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Abstract
Amplicon-based next-generation sequencing (NGS) has been widely adopted for genetic variation detection in human and other organisms. Conventional data analysis paradigm includes primer trimming before read mapping. Here we introduce BAMClipper that removes primer sequences after mapping original sequencing reads by soft-clipping SAM/BAM alignments. Mutation detection accuracy was affected by the choice of primer handling approach based on real NGS datasets of 7 human peripheral blood or breast cancer tissue samples with known BRCA1/BRCA2 mutations and >130000 simulated NGS datasets with unique mutations. BAMClipper approach detected a BRCA1 deletion (c.1620_1636del) that was otherwise missed due to edge effect. Simulation showed high false-negative rate when primers were perfectly trimmed as in conventional practice. Among the other 6 samples, variant allele frequencies of 5 BRCA1/BRCA2 mutations (indel or single-nucleotide variants) were diluted by apparently wild-type primer sequences from an overlapping amplicon (17 to 82% under-estimation). BAMClipper was robust in both situations and all 7 mutations were detected. When compared with Cutadapt, BAMClipper was faster and maintained equally high primer removal effectiveness. BAMClipper is implemented in Perl and is available under an open source MIT license at https://github.com/tommyau/bamclipper.
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