Process and annotate COSMIC Cancer Gene Census data for Hail-based multiomics variant analysis.
npx skills add https://github.com/bigbio/hvantk --skill cosmic-cgc
Please help me install this Agent Skill. Skill: cosmic-cgc Source: https://github.com/bigbio/hvantk/tree/main/hvantk/skills/cosmic_cgc Command: npx skills add https://github.com/bigbio/hvantk --skill cosmic-cgc
This skill addresses the complexity of integrating curated cancer gene data into multiomics pipelines, providing a standardized way to filter and analyze genes with causal roles in human cancer.
Use the hvantk reprocess cosmic-cgc:submissions command to build the annotated gene table from your raw input file.
High-intent search queries and answers about installing and using this skill.
You can integrate COSMIC CGC data into a Hail pipeline by using a specialized command to reprocess and annotate the raw dataset, generating a normalized Hail table with tier classifications and mutation contexts for multiomics workflows.
Yes, you can filter cancer genes by somatic mutation context and tier level using Hail. This approach enables precise subsetting of the CGC dataset to isolate genes with specific causal roles in human cancer for targeted analysis.
Resolving gene symbols to HGNC IDs for cancer genomics annotation is achieved programmatically during the COSMIC CGC data processing step, ensuring standardized gene identification and provenance-tracked output for reproducible research.
Yes, this COSMIC annotation approach supports filtering for oncogenes and tumor suppressor genes. It allows precise subsetting based on the specific role a gene plays in cancer, alongside mutation context and tier classifications.
To run Hail-based cancer variant annotation, you need the Hail framework and the pandas library installed. These dependencies facilitate the table operations and data normalization required for processing the CGC dataset.
Use Tier 1 somatic oncogene filtering for tumor sample variant datasets when you need to prioritize potential driver mutations. This filters the dataset to include only highly curated genes with established causal roles in human cancer.
OwnLabAIDownload COSMIC cancer mutation data files via authenticated Python requests.
bigbioPredict functional effects of genetic variants using the AlphaGenome API.
bigbioMap legacy gene symbols and aliases to canonical HGNC identifiers.
bigbioParse Ensembl GTF files into a per-gene Hail Table with structural and coordinate metadata.
