Queries NCBI ClinVar to retrieve and interpret clinical significance data for human genetic variants.
This skill provides a specialized interface for interacting with NCBI's ClinVar database, the primary archive for human genetic variation and its relationship to health. It enables researchers and developers to programmatically search variants via E-utilities API, process bulk datasets from FTP servers, and annotate VCF files with clinical pathogenicity classifications. By automating the interpretation of ACMG/AMP guidelines and star-rated evidence levels, it streamlines genomic medicine workflows and helps resolve conflicting variant interpretations within bioinformatics pipelines.
주요 기능
01Automated interpretation of pathogenicity classifications and star-rated review status
02Heuristics for resolving conflicting variant interpretations and tracking classification updates
03VCF file annotation and filtering integration with bcftools and Python
041 GitHub stars
05Programmatic access to NCBI E-utilities API for searching and fetching records
06Bulk data processing from FTP in XML, VCF, and tab-delimited formats
사용 사례
01Automating the retrieval of pathogenic variants for specific genes like BRCA1 or CFTR
02Annotating genomic variant call sets (VCF) with clinical significance data for diagnostic research
03Building and maintaining local bioinformatics databases by parsing monthly ClinVar XML releases
