liyao001/tabix

Note: tabix and bgzip binaries are now part of the HTSlib project.

tabix

Note: tabix and bgzip binaries are now part of the HTSlib project.

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.

What's new in this version?

Add swithes which can filter positions of a input table according to specific annotations indexed by tabix tool. The word "filter" means that you can keep those matched lines or discard those matched lines.

Options

• -p STR preset: gff, bed, sam, vcf, psltbl [gff]
• -s INT sequence name column [1]
• -b INT start column [4]
• -e INT end column; can be identical to '-b' [5]
• -S INT skip first INT lines [0]
• -c CHAR symbol for comment/meta lines [#]
• -r FILE replace the header with the content of FILE [null]
• -B region1 is a BED file (entire file will be read)
• -0 zero-based coordinate
• -h print also the header lines
• -H print only the header lines
• -l list chromosome names
• -f force to overwrite the index
• -F filter a table, which will print table lines which can be found in <in.tab.bgz> file to stdout
• -D along with -F, when -D opens, table lines which cannot be found in <in.tab.bgz> will be printed to stdout