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  • how to annotate somatic mutation?

    hi:
    I have map the tumor-normal pair exome data to genome using BWA and calling somatic mutation using Varcan. how to annotate somatic mutaion? just like classify the somatic mutation to missense_mutation or silent or frame_shift,etc.
    thanks in advance.

  • #2
    COSMIC: http://varianttools.sourceforge.net/Annotation/COSMIC

    SnpEff: http://snpeff.sourceforge.net/

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    • #3
      Online annotation tool VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/) capable of annotating millions of variants in minutes should be a good candidate to satisfy your expectation.

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      • #4
        If you have the VCF file, you can also use wAnnovar: http://wannovar.usc.edu/

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        • #5
          Ensembl VEP http://useast.ensembl.org/info/docs/...vep/index.html
          will perform annotation for all transcripts, provides precomputed sift/polyphen scores, and indicates which variants are in dbSNP (mostly germline with MAFreq) and COSMIC (mostly somatic). It will also annotate regulatory features.
          Last edited by m_two; 11-25-2013, 02:41 PM.

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          • #6
            Another tool you may be interested in: https://github.com/ckandoth/vcf2maf

            It uses snpEff to annotate all overlapping transcripts for each variant then filters the annotation to identify a single, best transcript isoform with the most severe effect and longest coding sequence.

            The prioritization considers transcript biotypes and attempts to avoid pseudogenes and incomplete ORFs.

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