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 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.
OPTIONS OF TABIX¶
- -p STR
- Input format for indexing. Valid values are: gff, bed, sam, vcf and
psltab. 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 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]
- -b INT
- Column of start chromosomal position. [4]
- -e INT
- Column of end chromosomal position. The end column can be the same as the
start column. [5]
- -S INT
- Skip first INT lines in the data file. [0]
- -c CHAR
- Skip lines started with character CHAR. [#]
- -0
- Specify that the position in the data file is 0-based (e.g. UCSC files)
rather than 1-based.
- -h
- Print the header/meta lines.
- -B
- The second argument is a BED file. When this option is in use, the input
file may not be sorted or indexed. The entire input will be read
sequentially. Nonetheless, with this option, the format of the input must
be specificed correctly on the command line.
- -f
- Force to overwrite the index file if it is present.
- -l
- List the sequence names stored in the index file.
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)