Can I download VCF files using this skill?

Yes, the skill provides shortcuts to download coding mutations in standard VCF format, which is compatible with tools like pysam, bcftools, and GATK.

Is a COSMIC account required to use this skill?

Yes, you must have a registered account at cancer.sanger.ac.uk. Access is free for academic users, while commercial users require a license.

How do I handle large file downloads from COSMIC?

The skill includes specialized scripts that handle large-scale data transfers and provide progress tracking for files that can often reach several gigabytes in size.

What kind of mutational signatures are available?

You can access Single Base Substitution (SBS), Doublet Base Substitution (DBS), and Insertion/Deletion (ID) signature definitions.

Which genome assemblies does this skill support?

It supports both the current GRCh38 standard and the legacy GRCh37 assembly, ensuring compatibility with older and newer research pipelines.

Cosmic Cancer Database Integration

Name: Cosmic Cancer Database Integration
Author: Activer007

byActiver007

Data Science & ML

Streamlines access to the COSMIC database for retrieving somatic mutations, cancer gene census lists, and mutational signatures for oncology research.

About

The Cosmic Database skill provides a robust interface for researchers and bioinformaticians to programmatically access the Catalogue of Somatic Mutations in Cancer (COSMIC). It automates the complex authentication and download processes for massive genomic datasets, including point mutations, structural variants, and drug resistance data. By supporting both GRCh38 and GRCh37 assemblies and offering pre-configured Python scripts for data manipulation, this skill significantly reduces the friction of integrating high-quality cancer genomics data into computational pipelines and precision oncology workflows.

Key Features

Direct retrieval of expert-curated Cancer Gene Census (CGC) data.
Access to comprehensive mutational signature profiles (SBS, DBS, and ID).
0 GitHub stars
Python-based helper functions for filtering mutations by gene, role, or cancer type.
Support for both GRCh38 and GRCh37 reference genome assemblies.
Automated multi-format data downloads (TSV, CSV, VCF) from COSMIC.

Use Cases

Building automated bioinformatics pipelines that require the latest somatic mutation data.
Cross-referencing experimental variants against known drug resistance mutations and clinical annotations.
Conducting large-scale genomic analysis to identify mutational signatures in cancer cohorts.

About

Key Features

Direct retrieval of expert-curated Cancer Gene Census (CGC) data.
Access to comprehensive mutational signature profiles (SBS, DBS, and ID).
0 GitHub stars
Python-based helper functions for filtering mutations by gene, role, or cancer type.
Support for both GRCh38 and GRCh37 reference genome assemblies.
Automated multi-format data downloads (TSV, CSV, VCF) from COSMIC.

Use Cases

Building automated bioinformatics pipelines that require the latest somatic mutation data.
Cross-referencing experimental variants against known drug resistance mutations and clinical annotations.
Conducting large-scale genomic analysis to identify mutational signatures in cancer cohorts.