ArticleBioinformatics (Oxford, England)2024
BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers, 4 of them syntheses that pooled it.
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Who cites it
84 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Contribution of copy number variants to schizophrenia in East Asian populations.Nature genetics · 2026Pooled it
- Multiancestry and Multitrait GWAS Meta-Analysis on Schizophrenia With a Sample of 322,321 Unveils Genetic Links to Chronic Lung Diseases.Genes, brain, and behavior · 2026Pooled it
- Trans-ancestry GWAS identifies 59 loci and improves risk prediction and fine-mapping for kidney stone disease.Nature communications · 2025Pooled it
- A multi-ancestry GWAS of Fuchs corneal dystrophy highlights the contributions of laminins, collagen, and endothelial cell regulation.Communications biology · 2024Pooled it
- DNA Repair gene alterations and efficacy from gemcitabine and nab-paclitaxel with/without durvalumab and tremelimumab in metastatic pancreatic ductal adenocarcinoma.Nature communications · 2026Trial
- Genome Wide Analysis Reveals Divergence and Ancestral Origins of Min Pigs.Animal genetics · 2026Article
- A multi-ancestry genome-wide association study of dry eye disease and systemic comorbidities.EBioMedicine · 2026Article
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- Genomic insights of first varicella zoster clade9 strain: a potential silent surge in Pakistan.Virus genes · 2026Article
- Recovering the precolonial population structure of Khoe-San descendant populations.Science advances · 2026Article
- Genetic interconnections between personality-related phenotypes and psychiatric disorders.European archives of psychiatry and clinical neuroscience · 2026Article
- Maternal immune activation disrupts epigenomic and functional maturation of cortical excitatory neurons.Molecular psychiatry · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.Cell genomics · 2026Article
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- Scoring Mating System of a Natural Population ofBiology · 2026Article
- VN1K is a pangenome-informed multi-omics and phenomics resource for the Vietnamese population.Nature communications · 2026Article
- Massively parallel characterization and predictive modelling of neuronal regulatory variation.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking long-read variant sensitivity across ONT and PacBio platforms using known clinically reported variants in a cohort of critically ill newborns.medRxiv : the preprint server for health sciences · 2026Article
- A chromatin-structure-guided framework for predictive and interpretable regulatory genomics.Briefings in bioinformatics · 2026Article
- Quantification and localization of integrated HIV-1 in memory and naïve CD4+ T cells from adolescents and young adults with perinatally-acquired HIV-1.PLoS pathogens · 2026Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
motivationMany genetics studies report results tied to genomic coordinates of a legacy genome assembly. However, as assemblies are updated and improved, researchers are faced with either realigning raw sequence data using the updated coordinate system or converting legacy datasets to the updated coordinate system to be able to combine results with newer datasets. Currently available tools to perform the conversion of genetic variants have numerous shortcomings, including poor support for indels and multi-allelic variants, that lead to a higher rate of variants being dropped or incorrectly converted. As a result, many researchers continue to work with and publish using legacy genomic coordinates.
resultsHere we present BCFtools/liftover, a tool to convert genomic coordinates across genome assemblies for variants encoded in the variant call format with improved support for indels represented by different reference alleles across genome assemblies and full support for multi-allelic variants. It further supports variant annotation fields updates whenever the reference allele changes across genome assemblies. The tool has the lowest rate of variants being dropped with an order of magnitude less indels dropped or incorrectly converted and is an order of magnitude faster than other tools typically used for the same task. It is particularly suited for converting variant callsets from large cohorts to novel telomere-to-telomere assemblies as well as summary statistics from genome-wide association studies tied to legacy genome assemblies. AVAILABILITY AND IMPLEMENTATION: The tool is written in C and freely available under the MIT open source license as a BCFtools plugin available at http://github.com/freeseek/score.
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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.