Which genome assemblies are supported by the COSMIC skill?

The skill supports both the current GRCh38 standard and the legacy GRCh37 assembly, allowing for compatibility with diverse bioinformatics pipelines.

Can I download data in VCF format?

Yes, the skill supports downloading mutation data in various formats, including TSV, CSV, and VCF for use with tools like pysam or GATK.

Does this skill require a COSMIC account?

Yes, authentication is required. Academic users can register for free at the COSMIC website, while commercial users must obtain a license from QIAGEN.

How do I ensure I am using the most recent cancer data?

The skill allows you to use a 'latest' shorthand in file paths, ensuring your scripts always retrieve the most recent quarterly release from COSMIC.

COSMIC Cancer Genomics

Name: COSMIC Cancer Genomics
Author: K-Dense-AI

byK-Dense-AI

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3,719

数据科学与机器学习

Accesses and queries the Catalogue of Somatic Mutations in Cancer (COSMIC) to retrieve high-quality genomic data for precision oncology and cancer research.

关于

The COSMIC Cancer Genomics skill enables researchers and bioinformaticians to programmatically interact with the world's most comprehensive resource for somatic mutation data. It facilitates the seamless download and analysis of curated gene lists, mutational signatures, structural variants, and drug resistance data directly within a coding workflow. By integrating COSMIC's extensive clinical annotations and the Cancer Gene Census, users can automate complex tasks such as variant filtering, target gene identification, and the analysis of cancer cell line genomics across both GRCh38 and GRCh37 assemblies.

主要功能

Automated retrieval of the expert-curated Cancer Gene Census (CGC)
Support for mutational signature profiles including SBS, DBS, and ID signatures
3,719 GitHub stars
Programmatic access to the world's largest somatic mutation database
Flexible data downloading for both GRCh38 and GRCh37 genome assemblies
Querying of structural variants, gene fusions, and copy number alterations

使用场景

Integrating curated drug resistance mutation data into bioinformatics pipelines for precision medicine
Analyzing mutational signatures to identify underlying carcinogenic processes in patient samples
Filtering clinical sequencing results against known oncogenes and tumor suppressors

关于

主要功能

Automated retrieval of the expert-curated Cancer Gene Census (CGC)
Support for mutational signature profiles including SBS, DBS, and ID signatures
3,719 GitHub stars
Programmatic access to the world's largest somatic mutation database
Flexible data downloading for both GRCh38 and GRCh37 genome assemblies
Querying of structural variants, gene fusions, and copy number alterations

使用场景

Integrating curated drug resistance mutation data into bioinformatics pipelines for precision medicine
Analyzing mutational signatures to identify underlying carcinogenic processes in patient samples
Filtering clinical sequencing results against known oncogenes and tumor suppressors