bedextract - manual page for bedextract 2.4.26+dfsg
version: 2.4.26 authors: Shane Neph & Alex Reynolds
- Every input file must be sorted per sort-bed.
- 0) --help or --version
- Print requested info and exit successfully
- 1) --list-chr <input.bed>
- Print all unique chromosome names found in
- 2) <chromosome> <input.bed>
- Retrieve all rows for chr8 with: bedextract chr8
- 3) <query.bed> <target>
- Grab elements from the <query.bed> that overlap
elements in <target>. Same as
- `bedops -e 1 <query.bed> <target>`,
except that this option fails silently
- if <query.bed> contains fully-nested BED elements. If
no fully-nested element exists, bedextract can vastly improve upon the
performance of bedops. <target> may be a BED or Starch file (with or
without fully-nested elements). Using '-' for <target> indicates
input (in BED format) comes from stdin.
The full documentation for bedextract
is maintained as a Texinfo manual.
If the info
programs are properly installed at
your site, the command
- info bedextract
should give you access to the complete manual.