Provided by: tabix_0.2.6-1git1_i386
bgzip - Block compression/decompression utility
tabix - Generic indexer for TAB-delimited genome position files
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 [...]]]
Tabix indexes a TAB-delimited genome position file in.tab.bgz and
creates an index file in.tab.bgz.tbi 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 overlapping 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.
OPTIONS OF TABIX
-p STR Input format for indexing. Valid values are: gff, bed, sam,
vcf and psltab. 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.
-s 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
-b INT Column of start chromosomal position. 
-e INT Column of end chromosomal position. The end column can be the
same as the start column. 
-S INT Skip first INT lines in the data file. 
-c CHAR Skip lines started with character CHAR. [#]
-0 Specify that the position in the data file is 0-based (e.g.
UCSC files) rather than 1-based.
-h Print the header/meta lines.
-B The second argument is a BED file. When this option is in
use, the input file may not be sorted or indexed. The entire
input will be read sequentially. Nonetheless, with this
option, the format of the input must be specificed correctly
on the command line.
-f Force to overwrite the index file if it is present.
-l List the sequence names stored in the index file.
(grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip >
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.
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.