Article

SafeMut: UMI-aware variant simulator incorporating allele-fraction overdispersion in read editing

2023-03-15

Abstract excerpt

Next-generation sequencing (NGS) has been widely used for calling biological variants. The gold-standard methodology for accessing the ability of a computational method to call a specific variant is to perform NGS wet-lab experiments on samples known to harbor this variant. Nevertheless, wet-lab experiments are both labor-intensive and time-consuming, and rare variants may not be present in a sample of population....

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: a1182c8e-d59f-58ab-813d-8fd5f66993f8
DOI: 10.1101/2023.03.14.532524

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

SafeMut: UMI-aware variant simulator incorporating allele-fraction overdispersion in read editingDOI 10.1101/2023.03.14.532524Read

Strelka2: Fast and accurate variant calling for clinical sequencing applicationsSemantic proximity Read

Strelka2: fast and accurate calling of germline and somatic variants.Semantic proximity Read

smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiersSemantic proximity Read

Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing dataSemantic proximity Read

A database of simulated tumor genomes towards accurate detection of somatic small variants in cancer.Semantic proximity Read

smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers.Semantic proximity Read

Calling small variants using universality with Bayes-factor-adjusted odds ratios.Semantic proximity Read

SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.Semantic proximity Read

Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractionsSemantic proximity Read

Accurate calling of low-frequency somatic mutations by sample-specific modeling of error ratesSemantic proximity Read

Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking.Semantic proximity Read

Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data.Semantic proximity Read