Jacques Dainat Bioinformatics Knowledge
Variant annotation
Initializing search
    knowledge
    • Home
    • Bioinformatics
    • Cluster
    • Programming
    • Resource
    • Sequencing
    • Statistics
    knowledge
    • Home
          • BAM / SAM
          • BED v1
          • CIGAR
          • CRAM v3.1
          • GFF / GTF all versions
          • Markdown
          • SUGAR
          • TEXTILE (Wiki)
          • VCF v4.4
          • VULGAR
          • Interesting ressources about formats
            • GTF
            • BED
          • FASTA
        • Genome
        • Mitochondrion
        • Chloroplast
        • Plasmid
      • Classification
      • Variant annotation
      • Visualisation
      • Schedulers commands comparison
      • Slurm
      • Rackham
      • Screen
        • Lecture
        • Cheat sheet
        • Useful commands
      • Bioconda
      • Git
        • Perl code profiler
      • Python
      • R
      • Nextflow
      • Course
      • Sites
      • Blogs
    • Sequencing
    • Statistics

    Variant annotation

    3 main tools exists :

    • Annovar
    • snpEff
    • VEP

    Choice of transcripts and software has a large effect on variant annotation, so choice in tool or reference annotation can be hard to do. Here a nice blog providing good insights.
    A new tool entered in the game called openCRAVAT. Official doc is here and the github account is here. Extra information can be found here.

    Previous
    Classification
    Next
    Visualisation
    Made with Material for MkDocs