Standalone command line tool to visualize coverage from a BAM file
Tinycov is a small standalone command line utility written in python to plot the coverage of a BAM file quickly. This software was inspired by Matt Edwards' genome coverage plotter.
To install the stable version:
pip3 install --user tinycov
To install the development version:
git clone https://github.com/cmdoret/tinycov.git cd tinycov pip install .
Only a BAM file alignment is required as input. If it is not coordinate-sorted, tinycov will make a sorted copy named
input.sorted.bam if the file is named
If no output is provided, the coverage plot will be displayed interactively using matplotlib. If
--out is used, the plot will be saved in a format determined by the output file's extension.
--text is provided, an output text file will be saved in the bedgraph format with overlapping windows (depending on the values of
Usage: tinycov.py [OPTIONS] BAM Options: -r, --res INTEGER Size of windows in which to compute coverage, in basepairs. [default: 10000] -s, --skip INTEGER Stride between windows, in basepairs. [default: 1000] -n, --name TEXT Name of the sample (plot title). Base name of input file by default -b, --blacklist TEXT Exclude those chromosomes from the plot. List of comma-separated chromosome names. -w, --whitelist TEXT Only include those chromosomes in the plot. List of comma-separated chromosome names. -o, --out PATH Output file where to write the plot. If not provided, the plot is shown interactively -t, --text PATH Output file where to write the raw data table. -p, --ploidy INTEGER Ploidy of input sample, used to estimate coverage threshold for aneuploidies --help Show this message and exit.
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