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1 .TH tabix 1 "3 February 2015" "htslib-1.2.1" "Bioinformatics tools"
2 .SH NAME
3 .PP
4 bgzip \- Block compression/decompression utility
5 .PP
6 tabix \- Generic indexer for TAB-delimited genome position files
7 .\"
8 .\" Copyright (C) 2009-2011 Broad Institute.
9 .\"
10 .\" Author: Heng Li <lh3@sanger.ac.uk>
11 .\"
12 .\" Permission is hereby granted, free of charge, to any person obtaining a
13 .\" copy of this software and associated documentation files (the "Software"),
14 .\" to deal in the Software without restriction, including without limitation
15 .\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
16 .\" and/or sell copies of the Software, and to permit persons to whom the
17 .\" Software is furnished to do so, subject to the following conditions:
18 .\"
19 .\" The above copyright notice and this permission notice shall be included in
20 .\" all copies or substantial portions of the Software.
21 .\"
22 .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
23 .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
24 .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
25 .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
26 .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
27 .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
28 .\" DEALINGS IN THE SOFTWARE.
29 .\"
30 .SH SYNOPSIS
31 .PP
32 .B bgzip
33 .RB [ -cdhB ]
34 .RB [ -b
35 .IR virtualOffset ]
36 .RB [ -s
37 .IR size ]
38 .RI [ file ]
39 .PP
40 .B tabix
41 .RB [ -0lf ]
42 .RB [ -p
43 gff|bed|sam|vcf]
44 .RB [ -s
45 .IR seqCol ]
46 .RB [ -b
47 .IR begCol ]
48 .RB [ -e
49 .IR endCol ]
50 .RB [ -S
51 .IR lineSkip ]
52 .RB [ -c
53 .IR metaChar ]
54 .I in.tab.bgz
55 .RI [ "region1 " [ "region2 " [ ... "]]]"
56
57 .SH DESCRIPTION
58 .PP
59 Tabix indexes a TAB-delimited genome position file
60 .I in.tab.bgz
61 and creates an index file (
62 .I in.tab.bgz.tbi
63 or
64 .I in.tab.bgz.csi
65 ) when
66 .I region
67 is absent from the command-line. The input data file must be position
68 sorted and compressed by
69 .B bgzip
70 which has a
71 .BR gzip (1)
72 like interface. After indexing, tabix is able to quickly retrieve data
73 lines overlapping
74 .I regions
75 specified in the format "chr:beginPos-endPos". Fast data retrieval also
76 works over network if URI is given as a file name and in this case the
77 index file will be downloaded if it is not present locally.
78
79 .SH INDEXING OPTIONS
80 .TP 10
81 .B -0, --zero-based
82 Specify that the position in the data file is 0-based (e.g. UCSC files)
83 rather than 1-based.
84 .TP
85 .BI "-b, --begin " INT
86 Column of start chromosomal position. [4]
87 .TP
88 .BI "-c, --comment " CHAR
89 Skip lines started with character CHAR. [#]
90 .TP
91 .BI "-C, --csi"
92 Skip lines started with character CHAR. [#]
93 .TP
94 .BI "-e, --end " INT
95 Column of end chromosomal position. The end column can be the same as the
96 start column. [5]
97 .TP
98 .B "-f, --force "
99 Force to overwrite the index file if it is present.
100 .TP
101 .BI "-m, --min-shift" INT
102 set minimal interval size for CSI indices to 2^INT [14]
103 .TP
104 .BI "-p, --preset " STR
105 Input format for indexing. Valid values are: gff, bed, sam, vcf.
106 This option should not be applied together with any of
107 .BR -s ", " -b ", " -e ", " -c " and " -0 ;
108 it is not used for data retrieval because this setting is stored in
109 the index file. [gff]
110 .TP
111 .BI "-s, --sequence " INT
112 Column of sequence name. Option
113 .BR -s ", " -b ", " -e ", " -S ", " -c " and " -0
114 are all stored in the index file and thus not used in data retrieval. [1]
115 .TP
116 .BI "-S, --skip-lines " INT
117 Skip first INT lines in the data file. [0]
118
119 .SH QUERYING AND OTHER OPTIONS
120 .TP
121 .B "-h, --print-header "
122 Print also the header/meta lines.
123 .TP
124 .B "-H, --only-header "
125 Print only the header/meta lines.
126 .TP
127 .B "-i, --file-info "
128 Print file format info.
129 .TP
130 .B "-l, --list-chroms "
131 List the sequence names stored in the index file.
132 .TP
133 .B "-r, --reheader " FILE
134 Replace the header with the content of FILE
135 .TP
136 .B "-R, --regions " FILE
137 Restrict to regions listed in the FILE. The FILE can be BED file (requires .bed, .bed.gz, .bed.bgz
138 file name extension) or a TAB-delimited file with CHROM, POS, and, optionally,
139 POS_TO columns, where positions are 1-based and inclusive. When this option is in use, the input
140 file may not be sorted.
141 regions.
142 .TP
143 .B "-T, --targets" FILE
144 Similar to
145 .B -R
146 but the entire input will be read sequentially and regions not listed in FILE will be skipped.
147 .PP
148 .SH EXAMPLE
149 (grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
150
151 tabix -p gff sorted.gff.gz;
152
153 tabix sorted.gff.gz chr1:10,000,000-20,000,000;
154
155 .SH NOTES
156 It is straightforward to achieve overlap queries using the standard
157 B-tree index (with or without binning) implemented in all SQL databases,
158 or the R-tree index in PostgreSQL and Oracle. But there are still many
159 reasons to use tabix. Firstly, tabix directly works with a lot of widely
160 used TAB-delimited formats such as GFF/GTF and BED. We do not need to
161 design database schema or specialized binary formats. Data do not need
162 to be duplicated in different formats, either. Secondly, tabix works on
163 compressed data files while most SQL databases do not. The GenCode
164 annotation GTF can be compressed down to 4%. Thirdly, tabix is
165 fast. The same indexing algorithm is known to work efficiently for an
166 alignment with a few billion short reads. SQL databases probably cannot
167 easily handle data at this scale. Last but not the least, tabix supports
168 remote data retrieval. One can put the data file and the index at an FTP
169 or HTTP server, and other users or even web services will be able to get
170 a slice without downloading the entire file.
171
172 .SH AUTHOR
173 .PP
174 Tabix was written by Heng Li. The BGZF library was originally
175 implemented by Bob Handsaker and modified by Heng Li for remote file
176 access and in-memory caching.
177
178 .SH SEE ALSO
179 .PP
180 .BR samtools (1)