Ubuntu Manpage: tabix - Generic indexer for TAB-delimited genome position files

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.

       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.

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, --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.

--cache INT
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.

--verbosity INT
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.

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;

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.