BEDEXTRACT(1)

NAME
bedextract - manual page for bedextract 2.4.42+dfsg

DESCRIPTION
bedextract

    citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract

    https://doi.org/10.1093/bioinformatics/bts277

version:
    2.4.42 (typical)

authors:
    Shane Neph & Alex Reynolds

    Every input file must be sorted per sort-bed.

    USAGE:

0) --help or --version
    Print requested info and exit successfully

1) --list-chr <input.bed>
    Print all unique chromosome names found in <input.bed>

2) <chromosome> <input.bed>
    Retrieve all rows for chr8 with: bedextract chr8 <input.bed>

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.

SEE ALSO
The full documentation for bedextract is maintained as a Texinfo manual. If the info and bedextract programs are properly installed at your site, the command

    info bedextract

should give you access to the complete manual.