NAME

       bedextract - manual page for bedextract 2.4.41+dfsg

DESCRIPTION

       bedextract

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

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

       version:
              2.4.41 (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.