Plot of coverage from bam file
Project description
BAM2PLOT
Plot your bam files!
bam2plot generates coverage plots:
... and if -c
is added, cumulative coverage plots for each reference (e.g. chromosomes) for each sample:
If the flag --highlight
is given, the regions with a coverage below the --treshold
are highlighted:
Below is an example of how bam2plot looks when runned in the terminal:
Dependencies
bam2plot
depends on perbase
, which you can install via:
cargo install perbase
# or
conda install -c bioconda perbase
Installation
You can install bam2plot
using the following pip command:
pip install bam2plot
Usage
Once installed, you can use the bam2plot
command to perform coverage analysis on BAM files and generate coverage plots. Here's how to use it:
usage: bam2plot [-h] -b BAM [-o OUTPATH] [-w WHITELIST] [-t THRESHOLD] [-r ROLLING_WINDOW]
[-i | --index | --no-index] [-s | --sort_and_index | --no-sort_and_index] [-z ZOOM]
[-l | --log_scale | --no-log_scale] [-c | --cum_plot | --no-cum_plot]
[-hl | --highlight | --no-highlight] [-p {png,svg,both}]
Plot your bam files!
options:
-h, --help show this help message and exit
-b BAM, --bam BAM bam file
-o OUTPATH, --outpath OUTPATH
Where to save the plots.
-w WHITELIST, --whitelist WHITELIST
Only include these references/chromosomes.
-t THRESHOLD, --threshold THRESHOLD
Threshold of mean coverage depth
-r ROLLING_WINDOW, --rolling_window ROLLING_WINDOW
Rolling window size
-i, --index, --no-index
Index bam file (default: False)
-s, --sort_and_index, --no-sort_and_index
Index and sort bam file (default: False)
-z ZOOM, --zoom ZOOM Zoom into this region. Example: -z='100 2000'
-l, --log_scale, --no-log_scale
Log scale of Y axis (default: False)
-c, --cum_plot, --no-cum_plot
Generate cumulative plots of all chromosomes (default: False)
-hl, --highlight, --no-highlight
Highlights regions where coverage is below treshold. (default: False)
-p {png,svg,both}, --plot_type {png,svg,both}
How to save the plots
Outputs
The BAM2Plot package generates coverage plots for each reference sequence in the BAM file. The plots are saved as SVG and PNG files in the specified output path or the default location.
Examples
Here's an example of how to use the BAM2Plot package:
bam2plot --bam input.bam --outpath output_folder --rolling_window 50 --threshold 5 -s -c -hl
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