DragonFly On-Line Manual Pages

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 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". 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
              columns, 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
       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)

htslib-1.3                     15 December 2015                       tabix(1)