alterlab-cosmic

You can download COSMIC cancer mutation data programmatically using a Python utility that authenticates with your COSMIC account credentials, resolves download URLs, and saves gzip-compressed TSV or VCF files with built-in error handling and versioned file paths.

Yes, you can fetch the Cancer Gene Census, mutational signatures, structural variants, copy number alterations, and resistance mutations programmatically alongside the core CosmicMutantExport.tsv.gz dataset.

Yes, the utility supports downloading COSMIC mutation data across both GRCh38 and GRCh37 pipelines, allowing you to fetch reference-appropriate files such as GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz for your analyses.

Yes, you need a COSMIC account because the Python utility requires your credentials to authenticate access before resolving and downloading the gzip-compressed mutation data files.

The utility saves downloaded COSMIC data as gzip-compressed TSV and VCF files, applying versioned file paths to ensure consistent tracking of mutation catalogs, structural variants, and copy number alterations.

Manual web downloads lack automated authentication, versioned file paths, and built-in error handling, making repetitive scripting and integration with Python data pipelines unreliable compared to programmatic access.