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
- 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-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.
- -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)