Format

meta:                                    # on peut mettre plein de metadatas clef / valeur
    created: "2012-04-21T18:25:43-05:00"  # Date au format iso 8601
    caller: "haplotypecaller"             # clef / valeur metadata
    fields:                              # listes des champs + description (obligatoire)
        - name: "ann1"
          description : "ann 1 description"
          visible: false
          index: 2                       # Pour mettre dans un ordre précis 

        - name: "ann2"
          description : "ann 2 description"
          visible: true
          index: 5
       
          samples:
             - name: "GT"
               description : "genotype"
             - name: "Af"
               description : "allele frequency of samples"
          
    samples:
        - Maman
        - Papa
        - Fiston

   
    sets:                                # Listes des sets de variants
        - name: denovo                    # Nom du set
          count : 242                     # Nombre de variant (optionnel)
        - variants:
            - 1
            - 12
            - 14
        - name: composite
          count : 242                     # Nombre de variant (optionnel)
 
        - variants:
            - 1
            - 12
            - 14  
         
 
variants :
    # Specification de SnpEff / et VEP
    # http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf?wb48617274=E051486A
    - id : 422                      # identifiant unique
      transcript:                  # identfiant du transcrit
      chr: "chr3"                   # chromosome
      pos: 234234                   # position
      ranking: 4                    # score ranking. en general ACMG 1-5
      comment: "test"               # Commentaire du variant
      impact: "HIGH"                # HIGH,MODERATE,LOW,MODIFIER
      c.dna: "c.324A>T"             # coding hgvs
      p.dna: "p.V680A"              # protein hgvs
      gene_name: "CFTR"             # Nom du gene
      gene_id: "ENSG0000000162"     # Id du gene
      effect: "stop_gained"         # term de sequence ontology
      feature: "transcripts"        # term de sequence ontology
      biotype: "coding"             # term de sequence ontology
     
    # Specification VCF
      ref: "rs213950"              # dbSNP id
      qual: 432                    # qualité score phred
      filter: "PASS"               # Pass filter
      af: 34                       # Allele frequency
      dp: 133                      # profondeur
     
     # Annotation custom
      ann1: "truc"
      ann2: "truc"
      ann3:                       # Commentaire par champs
        value: "ann3"
        comment: "commentaire"
        
    # Samples 
      samples : 
        - name: "Maman"
          gt: "0/1"
          af: 324
          dp: 24
        - name: "Papa"
          gt: "0/1"
          af: 324
          dp: 24
        - name: "Fiston"
          gt: "0/1"
          af: 324
          dp: 24