seqminer2

seqminer2 implements efficient querying and retrieval of sequence variants from biobank-scale sequencing datasets (millions of individuals, hundreds of millions of variants) to accelerate statistical genetics analyses.

Key Features:

• Variant-based indexing: Implements a variant-based indexing system specifically tailored for querying VCF/BCF files.
• Query speed: Provides query and retrieval speeds several magnitudes faster than tools that rely on tabix.
• Format support: Supports BGEN and PLINK file formats with reimplemented handlers for improved processing speed over alternative implementations.
• Biobank-scale handling: Scales to datasets encompassing millions of individuals and hundreds of millions of genetic variants.
• R integration: Provided as an R package for integration into R-based analysis workflows.
• Method development support: Facilitates method development, software prototyping, and extensive genomic data analysis within the R environment.

Scientific Applications:

• Method development: Supports development and benchmarking of new algorithms and software for genomic analyses.
• Software prototyping: Enables prototyping of analysis pipelines and tools that require rapid access to variant data.
• Statistical genetics analyses: Facilitates association studies and other statistical genetics analyses on biobank-scale sequence datasets.
• Genomic data exploration: Enables efficient exploration and retrieval of variants for downstream genomics research.

Methodology:

Implements a variant-based indexing system for querying VCF/BCF, includes reimplemented handlers for BGEN and PLINK, and benchmarks query/retrieval performance relative to tabix.