tabix(1) Bioinformatics tools tabix(1)NAME
bgzip - Block compression/decompression utility
tabix - Generic indexer for TAB-delimited genome position files
SYNOPSIS
bgzip [-cdhB] [-b virtualOffset] [-s size] [file]
tabix [-0lf] [-p gff|bed|sam|vcf] [-s seqCol] [-b begCol] [-e endCol]
[-S lineSkip] [-c metaChar] in.tab.bgz [region1 [region2 [...]]]
DESCRIPTION
Tabix indexes a TAB-delimited genome position file in.tab.bgz and cre‐
ates an index file ( in.tab.bgz.tbi or in.tab.bgz.csi ) when region is
absent from the command-line. The input data file must be position
sorted and compressed by bgzip which has a gzip(1) like interface.
After indexing, tabix is able to quickly retrieve data lines overlap‐
ping regions specified in the format "chr:beginPos-endPos". 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.
INDEXING OPTIONS-0, --zero-based
Specify that the position in the data file is 0-based (e.g.
UCSC files) rather than 1-based.
-b, --begin INT
Column of start chromosomal position. [4]
-c, --comment CHAR
Skip lines started with character CHAR. [#]
-C, --csi Skip lines started with character CHAR. [#]
-e, --end INT
Column of end chromosomal position. The end column can be the
same as the start column. [5]
-f, --force
Force to overwrite the index file if it is present.
-m, --min-shiftINT
set minimal interval size for CSI indices to 2^INT [14]
-p, --preset STR
Input format for indexing. Valid values are: gff, bed, sam,
vcf. This option should not be applied together with any of
-s, -b, -e, -c and -0; it is not used for data retrieval
because this setting is stored in the index file. [gff]
-s, --sequence INT
Column of sequence name. Option -s, -b, -e, -S, -c and -0 are
all stored in the index file and thus not used in data
retrieval. [1]
-S, --skip-lines INT
Skip first INT lines in the data file. [0]
QUERYING AND OTHER OPTIONS-h, --print-header
Print also the header/meta lines.
-H, --only-header
Print only the header/meta lines.
-l, --list-chroms
List the sequence names stored in the index file.
-r, --reheader FILE
Replace the header with the content of FILE
-R, --regions FILE
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 col‐
umns, where positions are 1-based and inclusive. When this
option is in use, the input file may not be sorted. regions.
-T, --targets FILE
Similar to -R but the entire input will be read sequentially and
regions not listed in FILE will be skipped.
EXAMPLE
(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;
NOTES
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 sup‐
ports 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.
AUTHOR
Tabix was written by Heng Li. The BGZF library was originally imple‐
mented by Bob Handsaker and modified by Heng Li for remote file access
and in-memory caching.
SEE ALSOsamtools(1)htslib-1.3 15 December 2015 tabix(1)
