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  • 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

  • #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

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    • #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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