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

ABSTRACT:

Background

With the rise of large-scale genome sequencing projects, genotyping of thousands of samples has produced immense variant call format (VCF) files. It is becoming increasingly challenging to store, transfer, and analyze these voluminous files. Compression methods have been used to tackle these issues, aiming for both high compression ratio and fast random access. However, existing methods have not yet achieved a satisfactory compromise between these 2 objectives.

Findings

To address the aforementioned issue, we introduce GSC (Genotype Sparse Compression), a specialized and refined lossless compression tool for VCF files. In benchmark tests conducted across various open-source datasets, GSC showcased exceptional performance in genotype data compression. Compared with

SUBMITTER: Luo X 

PROVIDER: S-EPMC11258903 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature