ArticlePLoS computational biology2015
Wham: Identifying Structural Variants of Biological Consequence.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
93 citing papers in PubMed.
- Structural Variants in the Human Genome Associated With Gut Microbiome and Blood Metabolic Traits With Potential Causal Links.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrated SNP and SV Analyses Reveal Genetic Mechanisms Underlying High-Altitude Adaptation in Goats.Animals : an open access journal from MDPI · 2026Article
- Germline determinants of risk and molecular subtype in young-onset lung cancer.medRxiv : the preprint server for health sciences · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- TriosCompass: a snakemake workflow for integrated detection of SNVs, indels, STRs, and structural de novo variants in parent-child trios.Bioinformatics (Oxford, England) · 2026Article
- Comprehensive analysis ofmedRxiv : the preprint server for health sciences · 2026Article
- Somatic structural variants drive upper tract urothelial carcinoma muscle invasiveness via activation of TPX2 transcription.EBioMedicine · 2026Article
- The biomedical landscape of genomic structural variation in the qatari population.Nature communications · 2026Article
- Jumping in the human brain: A review on somatic transposition.Fundamental research · 2026Review
- Article
- Modeling the long-range effect of an inversion downstream of EFNB1 concludes a 43-year molecular diagnostic odyssey for craniofrontonasal syndrome.European journal of human genetics : EJHG · 2025Article
- High-quality phased genome assemblies of line-bred Korean Hanwoo cattle.Scientific data · 2025Article
- CNPI: Rapid Analyses of Human Copy Number Data.Journal of molecular biology · 2025Article
- Haplotype-resolved genome and pan-genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens.iMetaOmics · 2025Article
- A Hitchhiker Guide to Structural Variant Calling: A Comprehensive Benchmark Through Different Sequencing Technologies.Biomedicines · 2025Article
- Whole genome sequencing and structural variations provide insights into the body size traits of Hu sheep.Scientific data · 2025Article
- Copy Number Variation Shapes Structural Genomic Diversity Associated With Ecological Adaptation in the Wild Tomato Solanum chilense.Molecular biology and evolution · 2025Article
- Pangenome discovery of missing autism variants.medRxiv : the preprint server for health sciences · 2025Article
- Genomic Analysis of Indel and SV Reveals Functional and Adaptive Signatures in Hubei Indigenous Cattle Breeds.Animals : an open access journal from MDPI · 2025Article
- A population-based analysis of the molecular landscape of glioma in adolescents and young adults reveals insights into gliomagenesis.Nature cancer · 2025Article
33 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate Wham's ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.
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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.