SNPack

SNPack provides compression and rapid retrieval of single nucleotide polymorphism (SNP) data to support large-scale genome-wide association studies (GWAS).

Key Features:

• Novel Compression Algorithm: Employs linkage disequilibrium block compression by representing blocks as differences relative to a reference SNP and compresses reference SNPs using call rate and minor allele frequency.
• Efficient Data Retrieval: Optimized for rapid decompression and fast loading of compressed SNP datasets.
• Competitive Performance: Demonstrated competitive compression rates and superior decompression speed on two SNP datasets compared to state-of-the-art software.
• Implementation: Compression and decompression algorithms are implemented as a C++ library.

Scientific Applications:

• Large-Scale Association Studies: Supports GWAS that investigate rare genetic variants and epistatic effects influencing complex phenotypic traits.
• Genomic Data Management: Enables efficient storage and retrieval of extensive SNP datasets to facilitate downstream genomic analyses.

Methodology:

Compression represents linkage disequilibrium blocks as differences relative to a reference SNP and compresses reference SNPs by exploiting call rate and minor allele frequency; algorithms for compression and decompression are implemented in C++.