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

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.

# 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

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

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.

来源信息