BGT

BGT encodes and queries whole-genome genotypes and haplotypes for large cohorts, enabling compact storage and high-throughput retrieval for genomic analyses.

Key Features:

• Compact file format: Encodes haplotypes and genotypes into a highly optimized binary representation that can store the haplotypes of 32,488 samples across 39.2 million SNPs in 7.4 GB.
• High-throughput decoding: Achieves decoding rates up to 420 million genotypes per CPU second.
• Real-time querying: Supports real-time responses to complex genotype queries across large datasets.
• Scalability for large cohorts: Designed to store and query whole-genome genotypes for tens to hundreds of thousands of samples.

Scientific Applications:

• Population genetics: Enables storage and querying of large-scale genotype and haplotype data for population structure and diversity analyses.
• Genome-wide association studies (GWAS): Supports retrieval of genotype data at scale for association testing across many samples and variants.
• Genotype frequency analyses: Facilitates computation and inspection of genotype and allele frequency distributions across large cohorts.

Methodology:

BGT encodes genomic data into a compact binary format and uses optimized algorithms for storage and fast retrieval/decoding (reported decoding rate up to 420 million genotypes per CPU second).