1 .TH tabix 1 "11 May 2010" "tabix-0.2.0" "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 Print the header/meta lines.
89 The second argument is a BED file. When this option is in use, the input
90 file may not be sorted or indexed. The entire input will be read sequentially. Nonetheless,
91 with this option, the format of the input must be specificed correctly on the command line.
94 Force to overwrite the index file if it is present.
97 List the sequence names stored in the index file.
101 (grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
103 tabix -p gff sorted.gff.gz;
105 tabix sorted.gff.gz chr1:10,000,000-20,000,000;
108 It is straightforward to achieve overlap queries using the standard
109 B-tree index (with or without binning) implemented in all SQL databases,
110 or the R-tree index in PostgreSQL and Oracle. But there are still many
111 reasons to use tabix. Firstly, tabix directly works with a lot of widely
112 used TAB-delimited formats such as GFF/GTF and BED. We do not need to
113 design database schema or specialized binary formats. Data do not need
114 to be duplicated in different formats, either. Secondly, tabix works on
115 compressed data files while most SQL databases do not. The GenCode
116 annotation GTF can be compressed down to 4%. Thirdly, tabix is
117 fast. The same indexing algorithm is known to work efficiently for an
118 alignment with a few billion short reads. SQL databases probably cannot
119 easily handle data at this scale. Last but not the least, tabix supports
120 remote data retrieval. One can put the data file and the index at an FTP
121 or HTTP server, and other users or even web services will be able to get
122 a slice without downloading the entire file.
126 Tabix was written by Heng Li. The BGZF library was originally
127 implemented by Bob Handsaker and modified by Heng Li for remote file
128 access and in-memory caching.