Standalone command line tool to visualize coverage from a BAM file
Project description
tinycov
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.
Installation
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 .
Input
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 input.bam
.
Output
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.
Additionally, if --text
is provided, an output text file will be saved in the bedgraph format with overlapping windows (depending on the values of --res
and --skip
).
Usage
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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