This module is currently in beta release. The module and/or documentation may be incomplete.
Convert BAM alignments to BED format.
Author: Chet Birger, Broad Institute
Contact: gp-help@broadinstitute.org
Algorithm Version:
Introduction
BEDTools.bamtobed is a conversion utility that converts sequence alignments in BAM format into BED and/or BEDPE records.
References
Parameters
| Name | Description |
|---|---|
| input file * | BAM file (-i) |
| edit distance | Convert BAM alignments to BED format using the BAM edit distance (NM) as the BED score. (-ed) |
| convert to bedpe | Convert BAM alignments to BEDPE (paired-end BED) format. (-bedpe) |
| additional command line options | Module will append these options to BEDTools bedtobam command line. See documentation for supported options. |
| output filename * | Output filename |
* - required
Input Files
-
input file
BAM file to be converted to BED format
Output Files
-
output filename
Resulting BED-formatted file.
Platform Dependencies
Task Type:
ChIP-Seq
CPU Type:
any
Operating System:
any
Language:
C++
Version Comments
| Version | Release Date | Description |
|---|---|---|
| 1 | 2013-12-12 | Initial version |