Filter BED by Proximity
Filter BED file using user-specified exclusion zone using the score column to determine which peak to retain.
File Inputs (BED)
This script processes BED-type files so make sure your input is properly formatted and uses the appropriate .bed or .bed.gz extension.
Filter Options
The 'Exclusion Distance' refers to the minimum distance (in base pairs) that another peak must be from a retained peak to be excluded.
Command Line Interface
Usage:
java -jar ScriptManager.jar peak-analysis filter-bed [-hV] [-e=<exclusion>]
[-o=<outputBasename>] <bedFile>
Positional Input
| Input | Description |
|---|---|
<bedFile> | The BED file we are filtering on |
Output Options
| Option | Description |
|---|---|
-o, --output=<outputBasename> | specify basename for output files (default=<bedFilename>_<exclusionNum>bp) |
-z, --gzip | gzip output (default=false) |
-e, --exclusion=<exclusion> | exclusion distance in bp (default=100) |