This module is currently in beta release. The module and/or documentation may be incomplete.
Combine overlapping or book-ended features in an interval file into a single feature which spans all of the combined features.
Author: Chet Birger, Broad Institute
Contact: gp-help@broadinstitute.org
Algorithm Version:
Introduction
bedtools.merge combines overlapping or “book-ended” features in a BED/GFF/VCF feature file into a single feature which spans all of the combined features. bedtools.merge requires that you presort your data by chromosome and then by start position.
References
Parameters
| Name | Description |
|---|---|
| input file * | Input BED/GFF/VCF file (-i) |
| force strandedness | Force strandedness; that is, only merge features that are on the same strand. (-s) |
| report number entries merged | Report the number of entries that were merged. 1 is reported if no merging occurred. (-n) |
| max distance for merge | Maximum distance between features (num base pairs) allowed for features to be merged. Default is 0. (-d) |
| report scores | Report scores of the merged features (-scores) |
| names | Report the names of the merged features separated by semicolons. (-nms) |
| output filename * | Output filename |
* - required
Input Files
-
input file
Input BED/GFF/VCF file
Output Files
-
output filename
Contents of output file are determined by the option selection; see BEDTools merge online documentation for descriptions of these output formats.
Platform Dependencies
Task Type:
ChIP-Seq
CPU Type:
any
Operating System:
any
Language:
C++
Version Comments
| Version | Release Date | Description |
|---|---|---|
| 1 | 2013-12-23 | Initial Beta version |