GEN2VCF

GEN2VCF converts IMPUTE GEN-format imputed genotype outputs into VCF files that include best-guess genotypes, genotype posterior probabilities, and genotype dosages for downstream genome-wide association studies (GWAS) analyses.

Key Features:

• Fast Conversion: Converts GEN to VCF at least 1.4 times faster than BCFtools, QCTOOL, and Oncofunco according to benchmark comparisons.
• Memory Efficiency: Uses up to 7.4 times less memory compared to alternative conversion tools.
• Comprehensive Output: Produces VCF output containing best-guess genotype, genotype posterior probabilities, and genotype dosage.
• Scalable Performance: Demonstrates consistent improvements in runtime and memory usage across sample sizes from 1,000 to 5,000.
• Pipeline Integration: Provides compatibility for integration with other software packages within genomic analysis pipelines.

Scientific Applications:

• Genome-wide association studies (GWAS): Facilitates conversion of imputed genotype data for downstream association analyses in GWAS.
• Large-scale genetic studies: Supports high-throughput processing required for large-scale genetic and imputation-based studies.

Methodology:

Performance was evaluated using a 1 Mb GEN-formatted file containing data from 5,000 samples with comparative tests across sample sizes from 1,000 to 5,000 to assess runtime and memory usage.