ArticleGenes & genomics2020
GEN2VCF: a converter for human genome imputation output format to VCF format.
Article in Genes & genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers, 1 of them a synthesis that pooled it.
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
4 citing papers in PubMed, 1 synthesis or guideline pooled it, 9 citations in OpenAlex.
- The contribution of common and rare genetic variants to variation in metabolic traits in 288,137 East Asians.Nature communications · 2022Pooled it
- SLC30A8 Rare Variant Modify Contribution of Common Genetic and Lifestyle Factors toward Type 2 Diabetes Mellitus.Diabetes & metabolism journal · 2026Article
- Genome-wide association study of therapeutic response to statin drugs in cardiovascular disease.Scientific reports · 2024Article
- Evaluating cardiovascular disease risk stratification using multiple-polygenic risk scores and pooled cohort equations: insights from a 17-year longitudinal Korean cohort study.Frontiers in genetics · 2024Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundFor a genome-wide association study in humans, genotype imputation is an essential analysis tool for improving association mapping power. When IMPUTE software is used for imputation analysis, an imputation output (GEN format) should be converted to variant call format (VCF) with imputed genotype dosage for association analysis. However, the conversion requires multiple software packages in a pipeline with a large amount of processing time.
objectiveWe developed GEN2VCF, a fast and convenient GEN format to VCF conversion tool with dosage support.
methodsThe performance of GEN2VCF was compared to BCFtools, QCTOOL, and Oncofunco. The test data set was a 1 Mb GEN-formatted file of 5000 samples. To determine the performance of various sample sizes, tests were performed from 1000 to 5000 samples with a step size of 1000. Runtime and memory usage were used as performance measures.
resultsGEN2VCF showed drastically increased performances with respect to runtime and memory usage. Runtime and memory usage of GEN2VCF was at least 1.4- and 7.4-fold lower compared to other methods, respectively.
conclusionsGEN2VCF provides users with efficient conversion from GEN format to VCF with the best-guessed genotype, genotype posterior probabilities, and genotype dosage, as well as great flexibility in implementation with other software packages in a pipeline.
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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.