ArticleBMC research notes2014
Genotype harmonizer: automatic strand alignment and format conversion for genotype data integration.
Article in BMC research notes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers, 7 of them syntheses that pooled it.
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Who cites it
91 citing papers in PubMed, 7 syntheses or guidelines pooled it.
- A genome-wide association study of buccal mucosa cancer in India and multi-ancestry meta-analysis discovers risk loci and gene-environment interactions.EBioMedicine · 2025Pooled it
- Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus.Nature communications · 2025Pooled it
- Large-scale GWAS of strabismus identifies risk loci and provides support for a link with maternal smoking.Nature communications · 2025Pooled it
- Pooled it
- A stop-gain variant inHGG advances · 2023Pooled it
- An integrative genomics approach identifies KDM4 as a modulator of trained immunity.European journal of immunology · 2022Pooled it
- Functional implications of disease-specific variants in loci jointly associated with coeliac disease and rheumatoid arthritis.Human molecular genetics · 2016Pooled it
- A randomized controlled trial of precision bezlotoxumab treatment for Clostridioides difficile infection.Cell reports. Medicine · 2026Trial
- The Soifua Manuia reference panel with 2,570 Samoan haplotypes improves genotype imputation quality among Samoans.Communications biology · 2026Article
- Structural Variant Imputation in Samoans Using a Population-Specific Reference Panel.medRxiv : the preprint server for health sciences · 2026Article
- Sex-stratified genetic regulators of cytokine production in the Dutch and Tanzanian populations.HGG advances · 2026Article
- Identification of SENP7 and UTF1/VENTX as new loci influencing clustered protocadherin methylation across blood and brain using a genome-wide association study.Molecular psychiatry · 2026Article
- Article
- Federated single-cell QTL meta-analysis reveals novel disease mechanisms.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide association study identifiesiScience · 2025Article
- High cell-type specificity of eQTLs revealed by single-nucleus analyses of brain and blood.bioRxiv : the preprint server for biology · 2025Article
- Admixture Mapping of Lipid Traits in Hispanic Americans.Journal of the American Heart Association · 2025Article
- The impact of interferon-γ pathway on trained immunity induction by vaccination with Bacille Calmette-Guérin.Scientific reports · 2025Article
- Enabling reproducible type 1 diabetes polygenic risk scoring for clinical and translational applications.medRxiv : the preprint server for health sciences · 2025Article
- Identifying individuals with rare disease variants by inferring shared ancestral haplotypes from SNP array data.NAR genomics and bioinformatics · 2025Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTo gain statistical power or to allow fine mapping, researchers typically want to pool data before meta-analyses or genotype imputation. However, the necessary harmonization of genetic datasets is currently error-prone because of many different file formats and lack of clarity about which genomic strand is used as reference.
findingsGenotype Harmonizer (GH) is a command-line tool to harmonize genetic datasets by automatically solving issues concerning genomic strand and file format. GH solves the unknown strand issue by aligning ambiguous A/T and G/C SNPs to a specified reference, using linkage disequilibrium patterns without prior knowledge of the used strands. GH supports many common GWAS/NGS genotype formats including PLINK, binary PLINK, VCF, SHAPEIT2 & Oxford GEN. GH is implemented in Java and a large part of the functionality can also be used as Java 'Genotype-IO' API. All software is open source under license LGPLv3 and available from http://www.molgenis.org/systemsgenetics.
conclusionsGH can be used to harmonize genetic datasets across different file formats and can be easily integrated as a step in routine meta-analysis and imputation pipelines.
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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.