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 creates an index file in.tab.bgz.tbi when region is absent from the com-
       mand-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. [gff]

       -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 retrieval.
		 [1]

       -b INT	 Column of start chromosomal position. [4]

       -e INT	 Column of end chromosomal position. The end column can be the same as the start column. [5]

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

       -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.

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 data-
       bases, 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 effi-
       ciently 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.

AUTHOR

       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.

SEE ALSO

       samtools(1)

tabix-0.2.0							    11 May 2010 							  tabix(1)