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논문 기본 정보

자료유형
학술저널
저자정보
Dong Mun Shin (Center for Genome Science National Institute of Health) Mi Yeong Hwang (Center for Genome Science National Institute of Health) Bong‑Jo Kim (Center for Genome Science National Institute of Health) Keun Ho Ryu (Faculty of Information Technology Ton Duc Thang University) Young Jin Kim (Center for Genome Science National Institute of Health)
저널정보
한국유전학회 Genes & Genomics Genes & Genomics Vol.42 No.10
발행연도
2020.1
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1,163 - 1,168 (6page)

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Background For 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. Objective We developed GEN2VCF, a fast and convenient GEN format to VCF conversion tool with dosage support. Methods The performance of GEN2VCF was compared to BCFtools, QCTOOL, and Oncofunco. The test data set was a 1 Mb GEN-formatted fle 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. Results GEN2VCF 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. Conclusions GEN2VCF provides users with efcient conversion from GEN format to VCF with the best-guessed genotype, genotype posterior probabilities, and genotype dosage, as well as great fexibility in implementation with other software packages in a pipeline.

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