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<ins>Note</ins>: 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.

<a name="description"></a>

Description

<a name="transformations"></a>Uses Gallia transformations

</a>to turn VCF rows such as:

<a name="input"></a>

#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:

<a name="output"></a>

{
  "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 }
}

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Clinvar References