Build GenCC gene-disease validity tables as Hail Tables for variant annotation.
npx skills add https://github.com/bigbio/hvantk --skill hvantk-resource-gencc
Please help me install this Agent Skill. Skill: hvantk:resource-gencc Source: https://github.com/bigbio/hvantk/tree/main/hvantk/skills/gencc Command: npx skills add https://github.com/bigbio/hvantk --skill hvantk-resource-gencc
This skill automates the complex lifecycle of onboarding, building, and updating Gene Curation Coalition (GenCC) submissions, ensuring your variant annotation pipelines use the most current and validated gene-disease validity assertions.
Use the hvantk reprocess gencc:submissions command to build the latest GenCC dataset from the raw source files.
High-intent search queries and answers about installing and using this skill.
To build GenCC gene-disease validity tables for variant annotation, use the automated build pipeline to transform raw GenCC TSV snapshots into high-performance Hail Tables keyed by gene, disease, and submitter.
To detect schema drift in GenCC data pipelines, use built-in drift detection mechanisms that monitor upstream GenCC data for schema changes or header modifications to prevent pipeline failures.
Yes, you need Hail to process GenCC submissions because the pipeline requires Hail for distributed data processing and integration with the hvantk plugin architecture to manage large genomic datasets.
To aggregate GenCC gene-disease assertions by submitting organization, use specialized streamer integration query methods designed to filter by submitter, classification level, or consensus thresholds.
Yes, you can use pandas and click alongside the automated build pipeline to manage GenCC data ingestion workflows, supporting schema validation and data transformation for genomic research pipelines.
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