This module is currently in beta release. The module and/or documentation may be incomplete.
Searches for closest overlapping features in A and B.
Author: Chet Birger, Broad Institute
Contact: gp-help@broadinstitute.org
Algorithm Version:
Introduction
BEDTools.closest searches for overlapping features in A and B. In the event that no feature in B overlaps the current feature in A, BEDTools.closest will report the closest (that is, least genomic distance from the start or end of A) feature in B. Note that BEDTools.closest will report an overlapping feature as the closest—that is, it does not restrict to closest non-overlapping feature.
References
Parameters
| Name | Description |
|---|---|
| input file A * | Input BED/GFF/VCF file A. (-a) |
| input file B * | Input BED/GFF/VCF file B. (-b) |
| force strandedness | Force strandedness; find the closest feature in B that overlaps A on the same strand. (-s) |
| report distance | Report distance as extra column. (-d) |
| ties * | How ties for closest feature should be handled. Occurs when two features in B have exactly same overlap with a feature in A. |
| output filename * | Output filename. |
* - required
Input Files
-
input file A
The first of two BED-, GFF- or VCF-formatted files containing annotation track data. -
input file B
The second of two BED-, GFF- or VCF-formated files containing annotation track data.
Output Files
-
output filename
A tab-delimeted txt file listing, for each feature in A, the closest feature in B.
Platform Dependencies
Task Type:
ChIP-Seq
CPU Type:
any
Operating System:
any
Language:
C++
Version Comments
| Version | Release Date | Description |
|---|