1 .TH tabix 1 "5 May 2010" "tabix-0.1.5" "Bioinformatics tools"
4 bgzip - Block compression/decompression utility
6 tabix - Generic indexer for TAB-delimited genome position files
32 .RI [ "region1 " [ "region2 " [ ... "]]]"
36 Tabix indexes a TAB-delimited genome position file
38 and creates an index file
42 is absent from the command-line. The input data file must be position
43 sorted and compressed by
47 like interface. After indexing, tabix is able to quickly retrieve data
50 specified in the format "chr:beginPos-endPos". Fast data retrieval also
51 works over network if URI is given as a file name and in this case the
52 index file will be downloaded if it is not present locally.
57 Input format for indexing. Valid values are: gff, bed, sam, vcf and
58 psltab. This option should not be applied together with any of
59 .BR \-s ", " \-b ", " \-e ", " \-c " and " \-0 ;
60 it is not used for data retrieval because this setting is stored in
64 Column of sequence name. Option
65 .BR \-s ", " \-b ", " \-e ", " \-S ", " \-c " and " \-0
66 are all stored in the index file and thus not used in data retrieval. [1]
69 Column of start chromosomal position. [4]
72 Column of end chromosomal position. The end column can be the same as the
76 Skip first INT lines in the data file. [0]
79 Skip lines started with character CHAR. [#]
82 Specify that the position in the data file is 0-based (e.g. UCSC files)
86 Force to overwrite the index file if it is present.
89 List the sequence names stored in the index file.
93 (grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
95 tabix -p gff sorted.gff.gz;
97 tabix sorted.gff.gz chr1:10,000,000-20,000,000;
100 It is straightforward to achieve overlap queries using the standard
101 B-tree index (with or without binning) implemented in all SQL databases,
102 or the R-tree index in PostgreSQL and Oracle. But there are still many
103 reasons to use tabix. Firstly, tabix directly works with a lot of widely
104 used TAB-delimited formats such as GFF/GTF and BED. We do not need to
105 design database schema or specialized binary formats. Data do not need
106 to be duplicated in different formats, either. Secondly, tabix works on
107 compressed data files while most SQL databases do not. The GenCode
108 annotation GTF can be compressed down to 4%. Thirdly, tabix is
109 fast. The same indexing algorithm is known to work efficiently for an
110 alignment with a few billion short reads. SQL databases probably cannot
111 easily handle data at this scale. Last but not the least, tabix supports
112 remote data retrieval. One can put the data file and the index at an FTP
113 or HTTP server, and other users or even web services will be able to get
114 a slice without downloading the entire file.
118 Tabix was written by Heng Li. The BGZF library was originally
119 implemented by Bob Handsaker and modified by Heng Li for remote file
120 access and in-memory caching.