Do I need an account to use the COSMIC skill?

Yes, COSMIC requires authentication. Academic users can register for free at the COSMIC website, while commercial users require a license from QIAGEN.

Is this skill suitable for clinical research pipelines?

Yes, it is designed to help bioinformaticians integrate authoritative COSMIC data into research pipelines for variant annotation and oncology analysis.

Can I download data in VCF format?

Yes, the skill supports downloading coding mutations in VCF format, as well as standard TSV and CSV files.

Which genome assemblies are supported?

The skill supports both the current GRCh38 (recommended) and the legacy GRCh37 reference genomes for all major data types.

What kind of specific cancer data can I retrieve?

You can access point mutations, indels, gene fusions, copy number alterations, mutational signatures, sample metadata, and the expert-curated Cancer Gene Census.

COSMIC Cancer Genomics Access

Name: COSMIC Cancer Genomics Access
Author: lifangda

bylifangda

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Data Science & ML

Accesses the world's largest somatic mutation database for cancer research and precision oncology data retrieval.

This skill provides a specialized interface for interacting with the COSMIC (Catalogue of Somatic Mutations in Cancer) database, allowing researchers and developers to programmatically download and analyze extensive cancer genomics data. It streamlines the retrieval of curated datasets including the Cancer Gene Census, mutational signatures, structural variants, and drug resistance mutations. By automating the authentication and file download processes, it enables seamless integration of high-quality somatic mutation data into bioinformatics pipelines, supporting tasks ranging from variant filtering to complex oncological analysis across both GRCh38 and GRCh37 assemblies.

Key Features

01Retrieval of mutational signature profiles including SBS, DBS, and ID signatures

02Access to drug resistance, copy number alterations, and gene fusion data

03Version management to ensure reproducibility by accessing specific COSMIC releases

0416 GitHub stars

05Automated downloading of somatic mutation data and Cancer Gene Census lists

06Support for multiple data formats including TSV, CSV, and VCF for bioinformatics tools

Use Cases

01Building bioinformatics pipelines to filter patient variants against known cancer-driving mutations

02Analyzing drug resistance mutations to support precision oncology and therapeutic research

03Researching mutational signatures to identify underlying causes of tumor development

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add lifangda/claude-plugins cosmic-database

For use in Claude.ai and ChatGPT

Download Skill