tabix

name	tabix
description	Use when you need to index or query tab-delimited genomic files for fast region-based retrieval.
disable-model-invocation	true
user-invocable	true

tabix

Quick Start

• Command: tabix [OPTIONS] [FILE] [REGION [...]]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/tabix
• Version: 1.22.1
• Full reference: See references/help.md

When To Use This Tool

• Index a sorted BGZF-compressed BED, GFF, VCF, GAF, or similar interval file for random access.
• Query one or more genomic regions without scanning the entire file.
• List contigs or print headers from an indexed genomics file.
• Use CSI instead of TBI when coordinates or contigs exceed classic tabix limits.

Common Patterns

# 1) Index a compressed VCF with the built-in preset
tabix -p vcf variants.vcf.gz

# 2) Query a region and keep the header
tabix -h variants.vcf.gz chr1:100000-110000

# 3) Pull many regions from a BED-like list
tabix -R regions.bed variants.vcf.gz > subset.vcf

# 4) Build a CSI index for large references or long coordinates
tabix -C -p bed intervals.bed.gz

Recommended Workflow

1. Sort the file by sequence and start coordinate, then compress it with bgzip.
2. Index with a preset like -p vcf whenever possible; fall back to explicit column settings only for custom tabular layouts.
3. Query exact regions, a regions file with -R, or a streaming targets file with -T depending on workload shape.
4. Keep the .tbi or .csi beside the data file so downstream tools can reuse the index.

Guardrails

• Input must be BGZF-compressed, not plain gzip-compressed.
• TBI is the default, but CSI is safer for large genomes, long contigs, or coordinates beyond the classic TBI range.
• -R uses indexed jumps, while -T streams through the file; pick the right mode for the number and distribution of intervals.
• Reindex after changing the file contents; stale indexes are a common silent failure mode.