NAME

       tabix - Generic indexer for TAB-delimited genome position files

SYNOPSIS

       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
       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 overlapping 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.

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

       -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-shift INT
                 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  columns,
              where  positions are 1-based and inclusive.  When this option is in use, the input file may not be
              sorted.

       -T, --targets FILE
              Similar to -R but the entire input will be read sequentially and regions not listed in  FILE  will
              be skipped.

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

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  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

       bgzip(1), samtools(1)