onkopus 0.1.5

Biomarker interpretation framework to analyze and interpret genetic alterations in cancer

Onkopus: A modular variant interpretation framework

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What is Onkopus?

Onkopus is an easy-to-use cancer variant interpretation framework to annotate, interpret and prioritize genetic alterations in cancer. Onkopus provides annotation for different mutation types including a wide range of features, including genomic, transcriptomic and protein information, biochemical features, pathogenicty prediction, functional effect prediction, biochemical features, and clinical significance of treatments on molecular targets.

Installation

Install the main Onkopus package:

python -m pip install onkopus

Usage

Use Onkopus from the command line

Onkopus provides a command line tool to directly annotate variant files. Run the onkopus tool by specifying an input file (-i) and the genome version (-g). Optionally pass an output file (-o) and specific modules (-m):

onkopus run -i somatic_mutations.vcf -g hg38

onkopus run -i somatic_mutations.vcf -g hg38 -m alphamissense
onkopus run -i somatic_mutations.vcf -g hg38 -m revel,primateai

Use Onkopus from Python

Use Onkopus from Python by running the full annotation pipeline or instantiate custom Onkopus clients and calling process_data:

import onkopus as op

genome_version="hg38"
bframe = op.read_file('./somatic_mutations.vcf', input_format='vcf')

# Annotate with ClinVar
client = op.ClinVarClient(genome_version=genome_version)
bframe.data = client.process_data(bframe.data)

# Annotate with REVEL
client = op.REVELClient(genome_version=genome_version)
bframe.data = client.process_data(bframe.data)

op.write_file('./somatic_mutations.annotated.vcf', bframe)

License

GPLv3

Documentation

The official documentation on how to use the Onkopus Python package is hosted on the public Onkopus website.

Public version

A public instance of Onkopus Web is available at https://mtb.bioinf.med.uni-goettingen.de/onkopus.