bedextract1

Overview

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.