Article

StableLift: Optimized Germline and Somatic Variant Detection Across Genome Builds

2024-11-03

Abstract excerpt

Reference genomes are foundational to modern genomics. Our growing understanding of genome structure leads to continual improvements in reference genomes and new genome “builds” with incompatible coordinate systems. We quantified the impact of genome build on germline and somatic variant calling by analyzing tumour-normal whole-genome pairs against the two most widely used human genome builds. The average individu...

Topics

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

Identifiers and source

Literature Corpus work: 0525b449-c438-5c4f-96a3-8c2026b6a6af
DOI: 10.1101/2024.10.31.621401

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

StableLift: Optimized Germline and Somatic Variant Detection Across Genome BuildsDOI 10.1101/2024.10.31.621401Read

ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers.Semantic proximity Read

The human pangenome reference reduces ancestry-related biases in somatic mutation detectionSemantic proximity Read

Donor-specific assemblies enhance somatic structural variant detection in complex genomic regionsSemantic proximity Read

The benefit of a complete reference genome for cancer structural variant analysisSemantic proximity Read

Standard operating procedure for somatic variant refinement of tumor sequencing dataSemantic proximity Read

TNscope: Accurate Detection of Somatic Mutations with Haplotype-based Variant Candidate Detection and Machine Learning FilteringSemantic proximity Read

Detection of somatic structural variants from short-read next-generation sequencing dataSemantic proximity Read

Structural Variant Breakpoint Detection with novoBreak.Semantic proximity Read

Detection of somatic structural variants from short-read next-generation sequencing data.Semantic proximity Read

Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read dataSemantic proximity Read

Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance.Semantic proximity Read

Improving long-read somatic structural variant calling with pangenome and de novo personal genome assemblySemantic proximity Read