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Question: Mutect v1 doesnt finds second alternative allele

mutect version 1 doesnt find any alternative allele than the first one. I use mutect 1 to find somatic variant calling. the reason i dont use mutect 2 is beacuse it produces too many false positives.

Thanks in advance


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @gufran

    We do not support mutect1 anymore. We can however help you with your mutect2 errors. Would you please be more specific and explain the issue you are facing with mutect2. What version of GATK are you using, please post the exact command and some examples of the false positives.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    We haven't heard from the user in more than two business days. The user has been notified and this ticket is now closed.

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