Note: This is only intended to showcase processing in Gallia, it is not complete nor thoroughly tested at the moment. Use output at your own risk.

See original announcement on BioStars. For more information, see gallia-core documentation, in particular the bioinformatics examples section.

Description

Uses Gallia transformations

to turn VCF rows such as:

#CHROM  POS      ID      REF  ALT  QUAL  FILTER  INFO
1       1049066  706774  G    A    .     .       AF_EXAC=0.00007;AF_TGP=0.00040;ALLELEID=694996;CLNDISDB=MONDO:MONDO:0014052,MedGen:C3808739,OMIM:615120;CLNDN=Myasthenic_syndrome,_congenital,_8;CLNHGVS=NC_000001.11:g.1049066G>A;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=AGRN:375790;MC=SO:0001627|intron_variant;ORIGIN=1;RS=201995572

into objects like:

{
  "CHROM": "1",
  "POS": 1049066,
  "_id": "706774",
  "REF": "G",
  "ALT": "A",
  "clinvar_allele_id": "694996",
  "HGVS_expression": "NC_000001.11:g.1049066G>A",
  "variation_review_status": "criteria_provided,_single_submitter",
  "clinical_significance": "Benign",
  "allele_origin": [ "germline" ],
  "disease": [
    { "preferred_name": "Myasthenic_syndrome,_congenital,_8",
      "terms": [
        { "database": "MONDO",
          "id": "MONDO:0014052" },
        { "database": "MedGen",
          "id": "C3808739" },
        { "database": "OMIM",
          "id": "615120" } ] } ],
  "genes": [
    { "symbol": "AGRN",
      "entrez": "375790" } ],
  "molecular_consequences": [
    { "term": "SO:0001627",
      "name": "intron_variant" } ],
  "variant_type": {
    "name": "single_nucleotide_variant",
    "term": "SO:0001483" },
  "AF": {
    "EXAC": 0.00007,
    "1KGP": 0.00040 }
}

Clinvar References

• AMA: Landrum MJ, Lee JM, Riley GR, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42(Database issue):D980-D985. doi:10.1093/nar/gkt1113
• MLA: Landrum, Melissa J et al. “ClinVar: public archive of relationships among sequence variation and human phenotype.” Nucleic acids research vol. 42,Database issue (2014): D980-5. doi:10.1093/nar/gkt1113
• APA: Landrum, M. J., Lee, J. M., Riley, G. R., Jang, W., Rubinstein, W. S., Church, D. M., & Maglott, D. R. (2014). ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic acids research, 42(Database issue), D980–D985. https://doi.org/10.1093/nar/gkt1113
• NLM: Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014 Jan;42(Database issue):D980-5. doi: 10.1093/nar/gkt1113. Epub 2013 Nov 14. PMID: 24234437; PMCID: PMC3965032.