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  • Varscan results annotation

    Hi,

    This is rather a simple problem but I have been unable to find a solution yet.

    Varscan (V.2.3.1) snp output has the strand information (eg. tumor_reads1_plus tumor_reads1_minus tumor_reads2_plus tumor_reads2_minus) and the nomenclature is not similar to the vcf headers. This being the requirement for the clinicians, I have chosen to use the varscan snp output (as opposed to using --output-vcf).

    However when using annovar as annotation tool (used awk to change some fields to make it compatible to annovar file.input), I still dont get any annotation results (all fields are listed in "summary-snp.annovar.invalid_input" and 0 in exome-summary or variant-function.

    Is there a work around for this or any other method to annotate varscan-snp output via annovar ?

    Any help is appreciated.

    Thanks

    Uma

  • #2
    Update - found a database solution to this

    Comment


    • #3
      Uma,

      Thanks for following up on this. You can rather easily convert VarScan's native output format to BED-like format to facilitate annotation, e.g.

      perl -pe '($chrom, $pos, $ref, $var) = split(/\t/, $_); $start = $pos - 1; $_ = "$chrom\t$start\t$pos\t$ref/$var\n"' varScan.output.snp >varScan.output.snp.bed

      We'll also look into expanding VCF output options to included the strand-specific read counts for somatic mutations. You mentioned this is required by clinicians... are their requirements written up somewhere?

      Yours,

      Dan Koboldt

      P.S. VarScan v2.3.1 was released on 8/9/12

      Comment


      • #4
        Hi Dan,

        Unfortunately not, its something I intend to develop just to make life simpler.

        Thanks for your reply.

        Uma

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