tabix

Genomic position file indexer

TLDR

Index a VCF file

$ tabix -p vcf [file.vcf.gz]

Index a BED file

$ tabix -p bed [file.bed.gz]

Index a GFF file

$ tabix -p gff [file.gff.gz]

Query a region

$ tabix [file.vcf.gz] [chr1:1000000-2000000]

Query with header output

$ tabix -h [file.vcf.gz] [chr1:1000000-2000000]

List chromosomes in index

$ tabix -l [file.vcf.gz]

Query regions from file

$ tabix -R [regions.bed] [file.vcf.gz]

Create CSI index for large chromosomes

$ tabix -C -p vcf [file.vcf.gz]

SYNOPSIS

tabix [options] file [region...]

tabix is a generic indexer for TAB-delimited genome position files. It creates an index that enables fast retrieval of data lines overlapping specified genomic regions.Input files must be position-sorted and compressed with bgzip. The index file (.tbi or .csi) enables random access to compressed data without decompressing the entire file.Common applications include indexing VCF variant files, BED annotation files, and GFF/GTF gene annotation files. The tool is essential for working with large genomic datasets in bioinformatics pipelines.Region queries use 1-based inclusive coordinates in the format chr:start-end.

PARAMETERS

-p, --preset format

Input format preset: gff, bed, sam, vcf.

-s, --sequence col

Column of sequence name (default: 1).

-b, --begin col

Column of start position (default: 4).

-e, --end col

Column of end position (default: 5).

-S, --skip-lines n

Skip first n lines.

-c, --comment char

Skip lines starting with character (default: #).

-0, --zero-based

Positions are 0-based half-open.

-C, --csi

Create CSI index instead of TBI.

-f, --force

Overwrite existing index.

-h, --print-header

Print header lines with output.

-H, --only-header

Print only header/meta lines.

-l, --list-chroms

List sequence names stored in the index file.

-r, --reheader file

Replace the header with the content of file.

-R, --regions file

Query regions from BED or TAB-delimited file.

-T, --targets file

Similar to -R but reads input sequentially.

-m, --min-shift INT

Set minimal interval size for CSI indices to 2^INT (default: 14).

-D

Do not download index file before opening (remote files only).

--separate-regions

Insert region name before each group in output.

--cache INT

Set BGZF block cache size in megabytes (default: 10).

INSTALL

sudo apt install tabix

sudo zypper install tabix

CAVEATS

Input must be bgzip-compressed, not gzip. TBI index format supports chromosomes up to 512 Mbp; use CSI (-C) for larger. Preset options cannot be combined with manual column specifications. The index stores column settings so retrieval doesn't need format specification.

HISTORY

tabix was developed by Heng Li and published in Bioinformatics journal in 2011. It is now part of the HTSlib project maintained by the samtools/htslib team. The tool has become a standard component in genomics workflows for efficient data access.