.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH BEDEXTRACT "1" "October 2018" "bedextract 2.4.35+dfsg" "User Commands"
.SH NAME
bedextract \- manual page for bedextract 2.4.35+dfsg
.SH DESCRIPTION
bedextract
.IP
citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
.IP
https://doi.org/10.1093/bioinformatics/bts277
.TP
version:
2.4.35 (typical)
.TP
authors:
Shane Neph & Alex Reynolds
.IP
Every input file must be sorted per sort\-bed.
.IP
USAGE:
.TP
0) \fB\-\-help\fR or \fB\-\-version\fR
Print requested info and exit successfully
.TP
1) \fB\-\-list\-chr\fR <input.bed>
Print all unique chromosome names found in <input.bed>
.TP
2) <chromosome> <input.bed>
Retrieve all rows for chr8 with:  bedextract chr8 <input.bed>
.TP
3) <query.bed> <target>
Grab elements from the <query.bed> that overlap elements in <target>. Same as
.TP
`bedops \fB\-e\fR 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.
.SH "SEE ALSO"
The full documentation for
.B bedextract
is maintained as a Texinfo manual.  If the
.B info
and
.B bedextract
programs are properly installed at your site, the command
.IP
.B info bedextract
.PP
should give you access to the complete manual.