xenial (1) tabix.1.gz

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.

       -i, --file-info
              Print file format info.

       -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)