ArticleNature communications2023
vcfdist: accurately benchmarking phased small variant calls in human genomes.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Aardvark: sifting through differences in a mound of variants.Genome biology · 2026Article
- A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology.mSystems · 2025Article
- Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance.Nature communications · 2025Article
- A comparison of short- and long-read whole genome sequencing for microbial pathogen epidemiology.bioRxiv : the preprint server for biology · 2025Article
- The impact of bioinformatic choices onMicrobiology spectrum · 2025Article
- Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions.bioRxiv : the preprint server for biology · 2025Article
- Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery.bioRxiv : the preprint server for biology · 2025Article
- Analysis and benchmarking of small and large genomic variants across tandem repeats.Nature biotechnology · 2025Article
- Article
- Are reads required? High-precision variant calling from bacterial genome assemblies.Access microbiology · 2025Article
- Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C data.Bioinformatics (Oxford, England) · 2024Article
- The GIAB genomic stratifications resource for human reference genomes.Nature communications · 2024Article
- Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data.eLife · 2024Article
- Jointly benchmarking small and structural variant calls with vcfdist.Genome biology · 2024Article
- Article
- VCF observer: a user-friendly software tool for preliminary VCF file analysis and comparison.BMC bioinformatics · 2024Article
- vcfdist: accurately benchmarking phased small variant calls in human genomes.Nature communications · 2023Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Accurately benchmarking small variant calling accuracy is critical for the continued improvement of human whole genome sequencing. In this work, we show that current variant calling evaluations are biased towards certain variant representations and may misrepresent the relative performance of different variant calling pipelines. We propose solutions, first exploring the affine gap parameter design space for complex variant representation and suggesting a standard. Next, we present our tool vcfdist and demonstrate the importance of enforcing local phasing for evaluation accuracy. We then introduce the notion of partial credit for mostly-correct calls and present an algorithm for clustering dependent variants. Lastly, we motivate using alignment distance metrics to supplement precision-recall curves for understanding variant calling performance. We evaluate the performance of 64 phased Truth Challenge V2 submissions and show that vcfdist improves measured insertion and deletion performance consistency across variant representations from R
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.