bgzip

bgzip is a compression utility that produces BGZF files, where BGZF stands for Block GZIP Format. It is designed for large genomic data files and is widely used in the HTSlib/Samtools ecosystem. BGZF compresses data in independent blocks, typically up to about 64 kilobytes of uncompressed data per block, and stores them sequentially in a single file. Each block is a gzip-compressed unit, and the collection of blocks is arranged to function as a single compressed file while enabling selective decompression.

The key feature of BGZF is support for random access to compressed data when combined with an index. In coordinate-sorted data such as VCF files, an index maps genomic coordinates to BGZF block offsets, allowing targeted retrieval of a region without decompressing the entire file. Tabix is commonly used to create such indexes (.tbi) for BGZF files, enabling fast querying of compressed data.

Usage and compatibility are straightforward. To compress a VCF file, one typically runs bgzip file.vcf, producing file.vcf.gz. Decompression can be performed with bgzip -d file.vcf.gz or with standard gzip tools for full-file extraction, though random access requires the BGZF index. To enable region queries, the corresponding index is created with tabix (e.g., tabix -p vcf file.vcf.gz).

BGZF is an industry-wide standard in genomic data processing within the Samtools/HTSlib ecosystem. It provides the familiar gzip compression while adding block-level structure and indexing to support fast, random access to large datasets.