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tabix \- Generic indexer for TAB-delimited genome position files

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.B tabix

.RB [ -0lf ]

.RB [ -p

gff|bed|sam|vcf]

.RB [ -s

.IR seqCol ]

.RB [ -b

.IR begCol ]

.RB [ -e

.IR endCol ]

.RB [ -S

.IR lineSkip ]

.RB [ -c

.IR metaChar ]

.I in.tab.bgz

.RI [ "region1 " [ "region2 " [ ... "]]]"

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Tabix indexes a TAB-delimited genome position file

.I in.tab.bgz

and creates an index file

.RI ( in.tab.bgz.tbi

or

.IR in.tab.bgz.csi )

when

.I region

is absent from the command-line. The input data file must be position

sorted and compressed by

.B bgzip

which has a

.BR gzip (1)

like interface.

After indexing, tabix is able to quickly retrieve data lines overlapping

.I regions

specified in the format "chr:beginPos-endPos".

(Coordinates specified in this region format are 1-based and inclusive.)

Fast data retrieval also

works over network if URI is given as a file name and in this case the

index file will be downloaded if it is not present locally.

The tabix

.RI ( .tbi )

and BAI index formats can handle individual chromosomes up to 512 Mbp

(2^29 bases) in length.

If your input file might contain data lines with begin or end positions

greater than that, you will need to use a CSI index.

.TP 10

Specify that the position in the data file is 0-based (e.g. UCSC files)

rather than 1-based.

.TP

Column of start chromosomal position. [4]

.TP

Skip lines started with character CHAR. [#]

.TP

Produce CSI format index instead of classical tabix or BAI style indices.

.TP

Column of end chromosomal position. The end column can be the same as the

start column. [5]

.TP

Force to overwrite the index file if it is present.

.TP

set minimal interval size for CSI indices to 2^INT [14]

.TP

Input format for indexing. Valid values are: gff, bed, sam, vcf.

This option should not be applied together with any of

.BR -s ", " -b ", " -e ", " -c " and " -0 ;

it is not used for data retrieval because this setting is stored in

the index file. [gff]

.TP

Column of sequence name. Option

.BR -s ", " -b ", " -e ", " -S ", " -c " and " -0

are all stored in the index file and thus not used in data retrieval. [1]

.TP

Skip first INT lines in the data file. [0]

.TP

Print also the header/meta lines.

.TP

Print only the header/meta lines.

.TP

List the sequence names stored in the index file.

.TP

Replace the header with the content of FILE

.TP

Restrict to regions listed in the FILE. The FILE can be BED file (requires .bed, .bed.gz, .bed.bgz

file name extension) or a TAB-delimited file with CHROM, POS, and, optionally,

POS_TO columns, where positions are 1-based and inclusive. When this option is in use, the input

file may not be sorted.

.TP

Similar to

.B -R

but the entire input will be read sequentially and regions not listed in FILE will be skipped.

.TP

Do not download the index file before opening it. Valid for remote files only.

.TP

Set the BGZF block cache size to INT megabytes. [10]

This is of most benefit when the

.B -R

option is used, which can cause blocks to be read more than once.

Setting the size to 0 will disable the cache.

.TP

This option can be used when multiple regions are supplied in the command line

and the user needs to quickly see which file records belong to which region.

For this, a line with the name of the region, preceded by the file specific

comment symbol, is inserted in the output before its corresponding group of

records.

.TP

Set verbosity of logging messages printed to stderr.

The default is 3, which turns on error and warning messages;

2 reduces warning messages;

1 prints only error messages and 0 is mostly silent.

Values higher than 3 produce additional informational and debugging messages.

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(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;

tabix -p gff sorted.gff.gz;

tabix sorted.gff.gz chr1:10,000,000-20,000,000;

It is straightforward to achieve overlap queries using the standard

B-tree index (with or without binning) implemented in all SQL databases,

or the R-tree index in PostgreSQL and Oracle. But there are still many

reasons to use tabix. Firstly, tabix directly works with a lot of widely

used TAB-delimited formats such as GFF/GTF and BED. We do not need to

design database schema or specialized binary formats. Data do not need

to be duplicated in different formats, either. Secondly, tabix works on

compressed data files while most SQL databases do not. The GenCode

annotation GTF can be compressed down to 4%. Thirdly, tabix is

fast. The same indexing algorithm is known to work efficiently for an

alignment with a few billion short reads. SQL databases probably cannot

easily handle data at this scale. Last but not the least, tabix supports

remote data retrieval. One can put the data file and the index at an FTP

or HTTP server, and other users or even web services will be able to get

a slice without downloading the entire file.

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Tabix was written by Heng Li. The BGZF library was originally

implemented by Bob Handsaker and modified by Heng Li for remote file

access and in-memory caching.

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.BR bgzip (1),

.BR samtools (1)