1tabix(1) Bioinformatics tools tabix(1)
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6 tabix - Generic indexer for TAB-delimited genome position files
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9 tabix [-0lf] [-p gff|bed|sam|vcf] [-s seqCol] [-b begCol] [-e endCol]
10 [-S lineSkip] [-c metaChar] in.tab.bgz [region1 [region2 [...]]]
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14 Tabix indexes a TAB-delimited genome position file in.tab.bgz and cre‐
15 ates an index file (in.tab.bgz.tbi or in.tab.bgz.csi) when region is
16 absent from the command-line. The input data file must be position
17 sorted and compressed by bgzip which has a gzip(1) like interface.
18 After indexing, tabix is able to quickly retrieve data lines overlap‐
20 ping regions specified in the format "chr:beginPos-endPos". (Coordi‐
21 nates specified in this region format are 1-based and inclusive.)
22 Fast data retrieval also works over network if URI is given as a file
24 name and in this case the index file will be downloaded if it is not
25 present locally.
26 The tabix (.tbi) and BAI index formats can handle individual chromo‐
28 somes up to 512 Mbp (2^29 bases) in length. If your input file might
29 contain data lines with begin or end positions greater than that, you
30 will need to use a CSI index.
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34 -0, --zero-based
35 Specify that the position in the data file is 0-based (e.g.
36 UCSC files) rather than 1-based.
37 -b, --begin INT
39 Column of start chromosomal position. [4]
40 -c, --comment CHAR
42 Skip lines started with character CHAR. [#]
43 -C, --csi Produce CSI format index instead of classical tabix or BAI
45 style indices.
46 -e, --end INT
48 Column of end chromosomal position. The end column can be the
49 same as the start column. [5]
50 -f, --force
52 Force to overwrite the index file if it is present.
53 -m, --min-shift INT
55 set minimal interval size for CSI indices to 2^INT [14]
56 -p, --preset STR
58 Input format for indexing. Valid values are: gff, bed, sam,
59 vcf. This option should not be applied together with any of
60 -s, -b, -e, -c and -0; it is not used for data retrieval be‐
61 cause this setting is stored in the index file. [gff]
62 -s, --sequence INT
64 Column of sequence name. Option -s, -b, -e, -S, -c and -0 are
65 all stored in the index file and thus not used in data re‐
66 trieval. [1]
67 -S, --skip-lines INT
69 Skip first INT lines in the data file. [0]
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73 -h, --print-header
74 Print also the header/meta lines.
75 -H, --only-header
77 Print only the header/meta lines.
78 -l, --list-chroms
80 List the sequence names stored in the index file.
81 -r, --reheader FILE
83 Replace the header with the content of FILE
84 -R, --regions FILE
86 Restrict to regions listed in the FILE. The FILE can be BED file
87 (requires .bed, .bed.gz, .bed.bgz file name extension) or a TAB-
88 delimited file with CHROM, POS, and, optionally, POS_TO col‐
89 umns, where positions are 1-based and inclusive. When this op‐
90 tion is in use, the input file may not be sorted.
91 -T, --targets FILE
93 Similar to -R but the entire input will be read sequentially and
94 regions not listed in FILE will be skipped.
95 -D Do not download the index file before opening it. Valid for re‐
97 mote files only.
98 --cache INT
100 Set the BGZF block cache size to INT megabytes. [10]
101 This is of most benefit when the -R option is used, which can
103 cause blocks to be read more than once. Setting the size to 0
104 will disable the cache.
105 --separate-regions
107 This option can be used when multiple regions are supplied in
108 the command line and the user needs to quickly see which file
109 records belong to which region. For this, a line with the name
110 of the region, preceded by the file specific comment symbol, is
111 inserted in the output before its corresponding group of
112 records.
113 --verbosity INT
115 Set verbosity of logging messages printed to stderr. The de‐
116 fault is 3, which turns on error and warning messages; 2 reduces
117 warning messages; 1 prints only error messages and 0 is mostly
118 silent. Values higher than 3 produce additional informational
119 and debugging messages.
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122 (grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip >
123 sorted.gff.gz;
124 tabix -p gff sorted.gff.gz;
126 tabix sorted.gff.gz chr1:10,000,000-20,000,000;
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131 It is straightforward to achieve overlap queries using the standard B-
132 tree index (with or without binning) implemented in all SQL databases,
133 or the R-tree index in PostgreSQL and Oracle. But there are still many
134 reasons to use tabix. Firstly, tabix directly works with a lot of
135 widely used TAB-delimited formats such as GFF/GTF and BED. We do not
136 need to design database schema or specialized binary formats. Data do
137 not need to be duplicated in different formats, either. Secondly, tabix
138 works on compressed data files while most SQL databases do not. The
139 GenCode annotation GTF can be compressed down to 4%. Thirdly, tabix is
140 fast. The same indexing algorithm is known to work efficiently for an
141 alignment with a few billion short reads. SQL databases probably cannot
142 easily handle data at this scale. Last but not the least, tabix sup‐
143 ports remote data retrieval. One can put the data file and the index at
144 an FTP or HTTP server, and other users or even web services will be
145 able to get a slice without downloading the entire file.
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149 Tabix was written by Heng Li. The BGZF library was originally imple‐
150 mented by Bob Handsaker and modified by Heng Li for remote file access
151 and in-memory caching.
152
155 bgzip(1), samtools(1)
156htslib-1.13 7 July 2021 tabix(1)