cnvkit

Copy number variant detection from targeted DNA sequencing

Command lineScience

Not tested on a device yet. What that means

Commands in the package

cnv_annotate.py
cnv_expression_correlate.py
cnv_updater.py
cnvkit.py
genome_instability_index.py
guess_baits.py
reference2targets.py
skg_convert.py
snpfilter.sh

About cnvkit

From Debian's package description

A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from targeted DNA sequencing. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

From Debian's description of the cnvkit package, under that package's license.

Dependencies

Depends on

python3-biopython
python3-matplotlib
python3-numpy
python3-pandas
python3-pomegranate
python3-pyfaidx
python3-pysam
python3-reportlab
python3-scipy
python3-sklearn
python3
r-bioc-dnacopy

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Sources and licenses

Name: the Debian package name.
Summary: Debian's short description of the cnvkit package, under that package's license.
Description: Debian's description of the cnvkit package, under that package's license.
Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
Popularity: Debian Popularity Contest counts.