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Tabix
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<h2 id="use">Use</h2> <p>Tabix requires the input file to be position-sorted and compressed using BGZF. After indexing, Tabix is able to retrieve data lines overlapping query <i>intervals</i> <i>regions</i> specified in the format "<i>chr:start-end</i>." The index files have a .tbi or .csi extension.<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> </p><p>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.<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/SAMtools/WFzNmNVs">SAMtools</a></li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="https://samtools.github.io/hts-specs/tabix.pdf">File format specification</a></li> <li><a href="https://www.htslib.org/doc/tabix.html">Command-line utility manual page</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Li, Heng (March 1, 2011). "Tabix: fast retrieval of sequence features from generic TAB-delimited files". Bioinformatics. 27 (5): 718–719. doi:10.1093/bioinformatics/btq671. ISSN 1367-4803. PMC 3042176. PMID 21208982. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042176" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042176</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>"VCF+tabix Track Format". UCSC Genome Browser. University of California, Santa Cruz. Retrieved January 26, 2021. <a href="https://genome.ucsc.edu/goldenPath/help/vcf.html" target="_blank">https://genome.ucsc.edu/goldenPath/help/vcf.html</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Buffalo, Vince (2015). "Out-of-Memory Approaches: Tabix and SQLite". Bioinformatics data skills (1st ed.). California: O'Reilly. p. 427. ISBN 978-1-4493-6737-4. OCLC 916120899. <a href="978-1-4493-6737-4" target="_blank">978-1-4493-6737-4</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>"Samtools/Htslib". GitHub. 2 May 2022. <a href="https://github.com/samtools/htslib/blob/develop/LICENSE" target="_blank">https://github.com/samtools/htslib/blob/develop/LICENSE</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>"tabix(1) manual page". www.htslib.org. Retrieved 2025-04-17. <a href="https://www.htslib.org/doc/tabix.html" target="_blank">https://www.htslib.org/doc/tabix.html</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>"tabix(1) manual page". www.htslib.org. Retrieved 2025-04-17. <a href="https://www.htslib.org/doc/tabix.html" target="_blank">https://www.htslib.org/doc/tabix.html</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>"tabix(1) manual page". www.htslib.org. Retrieved 2025-04-17. <a href="https://www.htslib.org/doc/tabix.html" target="_blank">https://www.htslib.org/doc/tabix.html</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> </ol>