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  • rnahar
    Junior Member
    • Aug 2013
    • 6
    #1

    VarScan Indels output to Annovar input

    Hi
    I am using Varscan for calling somatic SNPs and Indels and Annovar for annotation. However for indels the way it represents reference allele is 1 base upstream of the actual insertion/deletion. Is there a way to convert it to the annovar input format ?
    thanks
    Rahul
    Tags: None
    • m_two
      Member
      • Mar 2010
      • 50
      #2
      Is your problem the same as the one described here: http://seqanswers.com/forums/showthread.php?t=20000

      IsmailM posted a solution on 07-25-2013, 05:17 PM #19

        Comment

        • rnahar
          Junior Member
          • Aug 2013
          • 6
          #3
          My problem is the +/- in denoting indels as also discussed on the other thread - However I do not use the vcf output but standard tabular output so cannot use Ismail's solution. Will also post on the other thread.

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