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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

Uses Gallia transformations

to turn VCF INFO values such as:

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

AC=1;ANN=G|start_lost|HIGH|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>G|p.Met1?|1/918|1/918|1/305||,G-C|start_lost|HIGH|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>G|p.Leu1?|1/918|1/918|1/305||WARNING_REF_DOES_NOT_MATCH_GENOME,C|initiator_codon_variant|LOW|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>C|p.Met1?|1/918|1/918|1/305||;LOF=(OR4F5|ENSG00000186092|1|1.00)

into objects like:

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

{
  "AC": 1,
  "LOF": [
    { "Gene_Name": "OR4F5",
      "Gene_ID": "ENSG00000186092",
      "Number_of_transcripts_in_gene": 1,
      "Percent_of_transcripts_affected": 1.0 },
    { "Gene_Name": "OR4F5b",
      "Gene_ID": "ENSG00000186092b",
      "Number_of_transcripts_in_gene": 2,
      "Percent_of_transcripts_affected": 0.5 } ],
  "ANN": [
    {
      "Allele": "G",
      "Annotation": "start_lost",
      "Annotation_Impact": "HIGH",
      "Gene_Name": "OR4F5",
      "Gene_ID": "ENSG00000186092",
      "Feature_Type": "transcript",
      "Feature_ID": "ENST00000335137",
      "Transcript_BioType": "protein_coding",
      "Rank": {
        "value": 1,
        "total": 1 },
      "cDNA": {
        "pos": 1,
        "length": 918 },
      "CDS": {
        "pos": 1,
        "length": 918 },
      "AA": {
        "pos": 1,
        "length": 305 },
      "HGVS": {
        "c": "c.1A>G",
        "p": "p.Met1?" }
    },
    {
      "Allele": "G-C",
      "Annotation": "start_lost",
      "Annotation_Impact": "HIGH",
      "Gene_Name": "OR4F5",
      "Gene_ID": "ENSG00000186092",
      "Feature_Type": "transcript",
      "Feature_ID": "ENST00000335137",
      "Transcript_BioType": "protein_coding",
      "ERRORS_WARNINGS_INFO": "WARNING_REF_DOES_NOT_MATCH_GENOME",
      "Rank": {
        "value": 1,
        "total": 1 },
      "cDNA": {
        "pos": 1,
        "length": 918 },
      "CDS": {
        "pos": 1,
        "length": 918 },
      "AA": {
        "pos": 1,
        "length": 305 },
      "HGVS": {
        "c": "c.1A>G",
        "p": "p.Leu1?" }
    },
    {
      "Allele": "C",
      "Annotation": "initiator_codon_variant",
      "Annotation_Impact": "LOW",
      "Gene_Name": "OR4F5",
      "Gene_ID": "ENSG00000186092",
      "Feature_Type": "transcript",
      "Feature_ID": "ENST00000335137",
      "Transcript_BioType": "protein_coding",
      "Rank": {
        "value": 1,
        "total": 1 },
      "cDNA": {
        "pos": 1,
        "length": 918 },
      "CDS": {
        "pos": 1,
        "length": 918 },
      "AA": {
        "pos": 1,
        "length": 305 },
      "HGVS": {
        "c": "c.1A>C",
        "p": "p.Met1?" }
    }
  ]
}

<a name="references"></a>

SnpEff References