How does this skill help with VCF annotation?

It provides standardized patterns and commands for using tools like bcftools and Python to map ClinVar significance data and metadata onto your existing variant call sets.

How does the skill handle NCBI API rate limits?

It provides best practices for programmatic access, including the use of API keys to increase limits and implementing exponential backoff for stable data retrieval.

Can I use this for direct clinical diagnosis?

No, this skill is a research and development aid. Clinical interpretations should always be reviewed and validated by a qualified genetics professional.

Does it support both GRCh37 and GRCh38 assemblies?

Yes, the skill includes guidance and FTP paths for accessing ClinVar datasets mapped to both the GRCh37 (hg19) and GRCh38 (hg38) human genome assemblies.

ClinVar Database Assistant

Name: ClinVar Database Assistant
Author: Activer007

byActiver007

데이터 과학 및 ML

Queries NCBI ClinVar to retrieve genetic variant clinical significance, interpret pathogenicity, and annotate VCF files for genomic medicine.

소개

The ClinVar Database skill enables developers and researchers to integrate NCBI's comprehensive archive of human genetic variants and phenotypes directly into their workflows. It provides specialized guidance for searching variants by gene or condition, interpreting complex pathogenicity classifications (from Pathogenic to Benign), and accessing data programmatically via E-utilities or bulk FTP downloads. This skill is essential for bioinformatics pipelines requiring standardized variant classification, VCF annotation, and resolution of conflicting clinical interpretations based on ACMG/AMP guidelines and ClinVar star ratings.

주요 기능

Automate bulk data downloads in XML, VCF, and tab-delimited formats
Query ClinVar via web search patterns and E-utilities API
Resolve conflicting variant interpretations using star ratings and evidence
Interpret clinical significance using ACMG/AMP standardized terminology
0 GitHub stars
Annotate VCF files with clinical significance and review status

사용 사례

Automating the periodic update of local variant databases from ClinVar FTP releases
Developing bioinformatics pipelines to annotate patient VCF files with clinical significance
Researching high-confidence pathogenic variants in specific genes for study cohorts

소개

주요 기능

Automate bulk data downloads in XML, VCF, and tab-delimited formats
Query ClinVar via web search patterns and E-utilities API
Resolve conflicting variant interpretations using star ratings and evidence
Interpret clinical significance using ACMG/AMP standardized terminology
0 GitHub stars
Annotate VCF files with clinical significance and review status

사용 사례

Automating the periodic update of local variant databases from ClinVar FTP releases
Developing bioinformatics pipelines to annotate patient VCF files with clinical significance
Researching high-confidence pathogenic variants in specific genes for study cohorts