Bam-readcount is a utility that counts DNA sequence reads in BAM and CRAM files. It generates metrics for .bam files at single nucleotide positions:
Usage: bam-readcount [OPTIONS] <bam_file> [region]
Example: bam-readcount -f ref.fa some.bam
The output of bam-readcount is a no header tab-separated file end with .readcount. For more description of bam-readcount usage and output, please see the main github page of bam-readcount.
The bam-readcount image is located in the Boutros Lab Docker Hub repo here.
The main github page of bam-readcount can be found here with documentations. The official latest docker image is available here.
The Boutros lab docker image versioning standard here.
| Tool | Version |
|---|---|
| bam-readcount | 0.8.0 |
- Khanna, Ajay et al. “Bam-readcount -- rapid generation of basepair-resolution sequence metrics.” ArXiv arXiv:2107.12817v1. 27 Jul. 2021 Preprint.
Author: Caden Bugh, Mao Tian
docker-bam-readcount is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.
docker-bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions.
Copyright (C) 2021 University of California Los Angeles ("Boutros Lab") All rights reserved.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.