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  • vcf_consensus_error:Conflicting_variants

    Hi there,

    I'm trying to add indels from a vcf file, to the reference fasta file, in order to create a new reference. For that, I use bgzip, tabix and finally vcf-consensus tool. But I'm getting the following error:

    "Note: Conflicting variants at (or near) 'positionXXX', cannot apply both."

    Any ideas of the meaning of these error?

    Thanks

    Iran

  • #2
    Hey,

    Is it possible there is an insertion in one individual in a region deleted in another individual?

    Comment


    • #3
      Hi,
      I am also getting some problem while using vcf-consensus...
      i used command
      cat chr21.fa | vcf-consensus chr21_a.vcf.gz > chr21_ref21.fa

      but i got following error.

      The sequence "21" not found in the fasta file.

      can anyone help me to resolve this issue.

      Comment

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