Tabix Explained

Tabix is a free software utility for indexing TAB-delimited genome position files.^[1] It is commonly used in bioinformatics analysis to index large genomic data files such as GFF, VCF,^[2] or BED files for efficient data retrieval.^[3] Tabix was developed by Heng Li and is distributed under the MIT license.^{[4] [5]}

Use

Tabix requires the input file to be position-sorted and compressed using BGZF. After indexing, Tabix is able to retrieve data lines overlapping query intervals regions specified in the format "chr:start-end." The index files have a .tbi or .csi extension.

It also supports data retrieval over network using direct URL if the index is present in the same location or locally. It also supports multithreading for operations except listing of sequence names.

See also

• SAMtools

External links

• File format specification
• Command-line utility manual page

Notes and References

1. Li . Heng . March 1, 2011 . Tabix: fast retrieval of sequence features from generic TAB-delimited files . Bioinformatics . en . 27 . 5 . 718–719 . 10.1093/bioinformatics/btq671 . 1367-4803 . 3042176 . 21208982.
2. Web site: VCF+tabix Track Format . January 26, 2021 . . University of California, Santa Cruz.
3. Book: Buffalo, Vince . Bioinformatics data skills . 2015 . . 978-1-4493-6737-4 . 1st . California . 427 . Out-of-Memory Approaches: Tabix and SQLite . 916120899 . https://books.google.com/books?id=XxERCgAAQBAJ&pg=PA427.
4. Web site: Samtools/Htslib . . 2 May 2022 .
5. Web site: tabix(1) manual page . 2025-04-17 . www.htslib.org.