IMMerge

IMMerge merges large Variant Call Format (VCF) genotype files and preserves combined imputation quality information for merged genomic datasets.

Key Features:

• Scalability: Handles large-scale VCF genotype datasets, including data processed in batches.
• Multiprocessing: Uses Python's multiprocessing to parallelize merging and reduce computational time.
• Imputation quality handling: Combines imputation quality scores across datasets using Fisher's z transformation to correctly represent imputation measures in merged files.

Scientific Applications:

• Genome-wide association studies (GWAS): Supports merging genotype data and imputation quality metrics for combined-cohort GWAS analyses.
• Population genetics: Enables integration of batch-processed VCFs for population-level allele frequency, diversity, and structure studies.
• Personalized medicine: Facilitates consolidation of genotyped cohorts and imputation metrics to support variant interpretation in clinical and translational contexts.
• Downstream genomic analyses: Preserves imputation integrity to support downstream analyses that depend on accurate genotype and imputation quality information.

Methodology:

Merges VCF genotype files using parallel processing implemented with Python's multiprocessing and combines imputation quality scores via Fisher's z transformation.