skills/bioskills/bio-clinical-databases-clinvar-lookup/scripts/clinvar_query.py

• clinvar_summary · function · L25-L42 — def clinvar_summary(variation_id)
• car_id · function · L45-L54 — def car_id(hgvs_g)
• lookup_local_vcf · function · L57-L77 — def lookup_local_vcf(clinvar_vcf, chrom, pos, ref, alt)
• batch_resolve_to_car_then_clinvar · function · L80-L102 — def batch_resolve_to_car_then_clinvar(hgvs_list, sleep=0.34)
• filter_by_star_and_freshness · function · L105-L117 — def filter_by_star_and_freshness(df, min_star=2, max_age_months=36)
• parse_clnsig_conflict · function · L120-L148 — def parse_clnsig_conflict(clnsig_conf)
• annotate_vcf_with_bcftools · function · L151-L159 — def annotate_vcf_with_bcftools(input_vcf, clinvar_vcf, output_vcf)