GSC: efficient lossless compression of VCF files with fast query.

Area of Science:

• Bioinformatics
• Genomics
• Data Compression

Background:

• Large-scale genome sequencing generates massive Variant Call Format (VCF) files, posing storage and analysis challenges.
• Existing compression methods struggle to balance high compression ratios with fast random access for VCF data.

Purpose of the Study:

• Introduce Genotype Sparse Compression (GSC), a novel lossless compression tool specifically designed for VCF files.
• Evaluate GSC's performance against state-of-the-art compression tools for genomic data.

Main Methods:

• Developed GSC, a specialized lossless compression algorithm for VCF files.
• Conducted benchmark tests comparing GSC with GBC, GTC, gzip, zstd, and BCFtools on various open-source datasets.

Main Results:

• GSC achieved 26.9%–82.4% higher compression ratios compared to GBC and GTC.
• In lossless scenarios, GSC provided 1.5×–6.5× greater compression than general-purpose tools.
• GSC demonstrated competitive decompression query speeds and superior RAM usage, despite some trade-offs in decompression time.

Conclusions:

• GSC effectively balances high compression ratios with rapid data access, improving genomic data management.
• The tool supports seamless PLINK binary format conversion, facilitating downstream analyses.