https://github.com/jonas-fuchs/bamdash
create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
https://github.com/jonas-fuchs/bamdash
bam-files bed-files coverage-report dashboard genbank-files interactive plotly vcf-files
Last synced: 3 months ago
JSON representation
create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks
- Host: GitHub
- URL: https://github.com/jonas-fuchs/bamdash
- Owner: jonas-fuchs
- License: gpl-3.0
- Created: 2023-10-05T16:02:07.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2025-12-12T14:45:50.000Z (6 months ago)
- Last Synced: 2026-01-31T09:52:43.019Z (4 months ago)
- Topics: bam-files, bed-files, coverage-report, dashboard, genbank-files, interactive, plotly, vcf-files
- Language: Python
- Homepage:
- Size: 7.91 MB
- Stars: 57
- Watchers: 2
- Forks: 4
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://www.python.org/)
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://zenodo.org/badge/latestdoi/700952196)
[](https://pypi.org/project/bamdash/)
[](https://pypi.org/project/bamdash/)
[](https://anaconda.org/bioconda/bamdash)
[](https://anaconda.org/bioconda/bamdash)
## Overview
**BAMdash lets you create interactive coverage plots from your bam file with [`plotly`](https://plotly.com/)**
- **requires** only a `.bam`, `.bai` and the reference id to which the reads where mapped
- **create** a interactive `html` for data exploration
- **create** a static image (`jpg`, `png`, `pdf`, `svg`) ready for publication
- **add** additional tracks (supported: `.vcf`, `.gb`, `.bed`)
- **annotate** tracks with additional information
- **export** annoated track data as tabular files (`.bed`, `.vcf`) or json (`.gb`)
- **developed** for viral genomics
- **customize** all plotting parameters
**Feel free to report any bugs or request new features as issues!**
## Automatic annotation
BAMdash automatically computes serveral statistics:
- if `-bs` is > 1 it computes the mean over the bin size in the coverage plot
- for each track it computes recovery and mean coverage (set `-c` for the min coverage) for each element in the track
- if a `*.vcf` is provided it annotates `TRANSITION`/`TRANSVERSION` and type of exchange (`SNP`, `DEL`, `INS`)
If a `*.gb`and `*.vcf` is provided BAMdash computes if the mutations could have been caused by APOBEC deamination.
Moreover, it annotates the aminoacid exchange and the effect in the CDS (inspired by but not as powerful as [snpeff](http://pcingola.github.io/SnpEff/snpeff)). SNP and INDEL vcf annotation supports:
- `START_LOST`: INDEL or SNP start at the CDS and result in a start loss
- `STOP_LOST`: INDEL or SNP result in the loss of the stop codon
- `STOP_GAINED`: INDEL or SNP result in an additional stop codon
- `SYN`: SNP does not lead to an amino acid change
- `NON-SYN`: SNP leads to an amino acid change
- `AC_INSERTION`: INS that does not change already present amino acids
- `AC_CHANGE+AC_INSERTION`: INS where the affected codon is also non-syn
- `AC_DELETION`: DEL that does not change already present amino acids
- `AC_CHANGE+AC_DELETION`: DEL where the affected codon is also non-syn
- `FRAMESHIFT`: INDEL that leads to a frameshift
The nomenclature for the aminoacid effect is pretty simplified:
- `A58Y` - Exchange at pos 58 from A to Y
- `A58YY`- Exchange at pos 58 from A to Y and insertion of an additional Y
- `AF58Y`- Exchange at pos 58 from A to Y and deletion of the following F
- `A58fsX` - Frameshift at pos 58
## Example
## Installation
### via pip (recommened):
```shell
pip install bamdash
```
### via conda:
```shell
conda install -c bioconda bamdash
```
### For development:
```shell
git clone https://github.com/jonas-fuchs/BAMdash
cd BAMdash
pip install .
```
```shell
bamdash -v
```
You should see the current BAMdash version.
## Usage
```shell
usage:
bamdash -b bam_file_path -r reference_id [additional arguments]
```
```
full usage:
-h, --help show this help message and exit
-b , --bam bam file location
-r , --reference seq reference id
-q 15, --quality-threshold 15
qaulity threshold for reads
-bs , --binsize bins for the coverage plot
-t [track_1 ...], --tracks [track_1 ...]
file location of tracks
-c 5, --coverage 5 minimum coverage
--slider, --no-slider
show slider (default: False)
-e None, --export_static None
export as png, jpg, pdf, svg
-d px px, --dimensions px px
width and height of the static image in px
--dump, --no-dump dump annotated track data (default: False)
-v, --version show program's version number and exit
```
## Test BAMdash
- download the HEV example data:
https://zenodo.org/api/records/10159816/files-archive
- extract data, cd to folder and use bamdash:
```shell
bamdash -b HEV.bam -r HEV-pat-1 -t HEV.vcf HEVprim.bed HEVamp.bed HEV.gb
```
## Cutomization
BAMcov plotting settings can be adjusted in in the `config.py`. Therefore, you have to clone this repo.
Go to the configs location:
```shell
cd BAMdash/bamdash/scripts/
```
And open the `config.py` with a text editor, e.g.:
```shell
gedit config.py
```
and adjust the settings:
```python
# pdf settings
show_log = True
# overall layout
vcf_track_proportion = 0.3
gb_track_proportion = 0.5
bed_track_proportion = 0.2
plot_spacing = 0.05
# coverage customize
coverage_fill_color = "rgba(255, 212, 135, 0.2)"
coverage_line_color = "rgba(224, 168, 68, 1)"
average_line_color = "grey"
average_line_width = 1
# track customize
track_color_scheme = "agsunset" # for mutiple annotations tracks (genebank)
track_color_single = "rgb(145, 145, 145)" # for single tracks (any rgb value, but no named colors)
strand_types = ["triangle-right", "triangle-left", "diamond-wide"] # +, -, undefined strand
strand_marker_size = 8
strand_marker_line_width = 1
strand_marker_line_color = "rgba(0, 0, 0, 0.2)"
box_bed_alpha = [0.6, 0.6] # alpha values for boxes (bed)
box_bed_size = [0.4, 0.4] # size values for boxes (bed)
box_gb_alpha = [0.6, 0.8] # alpha values for boxes (gb)
box_gb_size = [0.4, 0.3] # size values for boxes (gb)
# variant customize
variant_marker_size = 13
variant_marker_line_width = 1
variant_line_color = "black"
stem_color = "grey"
stem_width = 1
snp_color = "grey"
ins_color = "blue"
del_color = "red"
```
To apply these new settings just repeat the installation procedure in the BAMdash dir:
```shell
pip install .
```
---
**Important disclaimer:**
*The code is under the GPLv3 licence. The code is WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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 3 of the License, or
(at your option) any later version.*