bgzip - Block compression/decompression utility
tabix - Generic indexer for TAB-delimited genome position files
Copyright (C) 2009-2011 Broad Institute.
Author: Heng Li <lh3@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
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 " [ ... "]]]"
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.
10 -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]
"-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.
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.
samtools (1)