bgzip

name	bgzip
description	Use when you need to compress or decompress files using BGZF (Blocked GNU Zip Format), create BGZF indexes for random access, or prepare bioinformatics files for tabix indexing.
disable-model-invocation	true
user-invocable	true

bgzip

Block compression utility from htslib that creates BGZF-compressed files suitable for random access and indexing.

Quick Start

• Command: bgzip [OPTIONS] [FILE]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bgzip
• Version: 1.22.1
• Full reference: See references/help.md for complete options and usage

When To Use This Tool

• Compress tabular genomics files into BGZF rather than ordinary gzip.
• Prepare files for random access and indexing in the HTS ecosystem.
• Reindex or integrity-check an existing BGZF file.
• Use it before tabix or other tools that require BGZF-aware random access.

Common Patterns

# 1) Compress and create a BGZF index
bgzip -i variants.vcf

# 2) Write compressed output while preserving the original file
bgzip -c variants.vcf > variants.vcf.gz

# 3) Reindex an existing BGZF file
bgzip -r variants.vcf.gz

# 4) Test file integrity
bgzip -t variants.vcf.gz

Recommended Workflow

1. Use BGZF, not generic gzip, for files that must support random access.
2. Create or refresh .gzi indexes when the compressed file changes.
3. Test integrity before feeding compressed files into downstream indexing or querying steps.
4. Keep compression and indexing steps explicit in pipelines.

Guardrails

• BGZF is gzip-compatible for decompression but not interchangeable with ordinary gzip for random-access workflows.
• -i creates a .gzi during compression; -r rebuilds the index later.
• -c writes to stdout and keeps the input file unchanged.
• Threading with -@ is useful for bigger files, but remember that downstream tools still need the final .gzi or tabix index.