Package org.monarchinitiative.lirical.core.model

Interface TranscriptAnnotation

public interface TranscriptAnnotation
The interface represents variant functional annotation data required by LIRICAL.

  • Method Details

    • getGeneId

      org.monarchinitiative.phenol.annotations.formats.GeneIdentifier getGeneId()
      Returns:
      gene identifier of the transcript.

    • getAccession

      String getAccession()
      Returns:
      transcript accession (e.g. NM_000130.4).

    • getVariantEffects

      List<de.charite.compbio.jannovar.annotation.VariantEffect> getVariantEffects()
      Returns:
      list of variant effects (e.g. MISSENSE_VARIANT).

    • getMostPathogenicVariantEffect

      default de.charite.compbio.jannovar.annotation.VariantEffect getMostPathogenicVariantEffect()
      Returns:
      the most pathogenic variant effect.

    • getVariantEffect

      String getVariantEffect()
      Returns:
      string of variant effects joined by + character.

    • getHgvsCdna

      String getHgvsCdna()
      Returns:
      effect of the variant on the cDNA sequence in HGVS format (e.g. c.578G>T).

    • getHgvsProtein

      String getHgvsProtein()
      Returns:
      effect of the variant on the protein sequence in HGVS format (e.g. p.(Cys193Phe)).