tabix - Generic indexer for TAB-delimited genome position files

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.

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.

       The tabix (.tbi) and BAI index formats can handle individual chromosomes up to 512 Mbp  (2^29  bases)  in
       length.   If  your input file might contain data lines with begin or end positions greater than that, you
       will need to use a CSI index.

       Multiple threads can be used for operations except listing of sequence names.

Example

       (grep "^#" in.gff; grep -v "^#" in.gff | sort -t"`printf '\t'`" -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;

Indexing Options

-0,--zero-based
                 Specify that the position in the data file is 0-based half-open (e.g. UCSC files)  rather  than
                 1-based.

       -b,--beginINT
                 Column of start chromosomal position. [4]

       -c,--commentCHAR
                 Skip lines started with character CHAR. [#]

       -C,--csi Produce CSI format index instead of classical tabix or BAI style indices.

       -e,--endINT
                 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,--presetSTR
                 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,--sequenceINT
                 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-linesINT
                 Skip first INT lines in the data file. [0]

Name

       tabix - Generic indexer for TAB-delimited genome position files

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.

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,--reheaderFILE
Replace the header with the content of FILE

-R,--regionsFILE
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,--targetsFILE
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.

--cacheINT
Set the BGZF block cache size to INT megabytes. [10]

This is of most benefit when the -R option is used, which can cause blocks to be read more than
once. Setting the size to 0 will disable the cache.

--separate-regions
This option can be used when multiple regions are supplied in the command line and the user needs
to quickly see which file records belong to which region. For this, a line with the name of the
region, preceded by the file specific comment symbol, is inserted in the output before its
corresponding group of records.

--verbosityINT
Set verbosity of logging messages printed to stderr. The default is 3, which turns on error and
warning messages; 2 reduces warning messages; 1 prints only error messages and 0 is mostly silent.
Values higher than 3 produce additional informational and debugging messages.

-@,--threadsINT
Set number of threads to use for the operation. The default is 0, where no extra threads are in
use.

Synopsis

tabix  [-0lf]  [-p  gff|bed|sam|vcf]  [-sseqCol]  [-bbegCol]  [-eendCol] [-SlineSkip] [-cmetaChar]
       in.tab.bgz [region1 [region2 [...]]]