GEN2VCF: a converter for human genome imputation output format to VCF format

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Genotype imputation is crucial for enhancing association mapping power in human genome-wide association studies.
• Converting IMPUTE software's GEN format output to VCF with genotype dosage is necessary for downstream analysis.
• Current conversion methods involve multiple software packages and extensive processing time.

Purpose of the Study:

• To develop GEN2VCF, a novel tool for rapid conversion of GEN format files to VCF format.
• To provide dosage support for imputed genotypes within the VCF output.

Main Methods:

• GEN2VCF performance was evaluated against BCFtools, QCTOOL, and Oncofunco.
• Tests utilized a 1 Mb GEN-formatted file with sample sizes ranging from 1000 to 5000.
• Performance metrics included runtime and memory usage.

Main Results:

• GEN2VCF demonstrated significantly improved performance in both runtime and memory usage.
• Runtime was at least 1.4-fold lower, and memory usage was at least 7.4-fold lower compared to other tested methods.
• These improvements were consistent across various sample sizes.

Conclusions:

• GEN2VCF offers efficient GEN to VCF conversion with essential genetic data, including best-guessed genotypes, posterior probabilities, and genotype dosage.
• The tool enhances flexibility for integration into existing bioinformatics pipelines.
• GEN2VCF is a valuable asset for researchers conducting genome-wide association studies.