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Somatic Variant Calling with Tumor Samples Only


I recently went to the workshop for variant calling and mentioned that I would like to perform somatic variant calling with Mutect using only tumor samples (no matched normal sample). I was told that there is a pipeline under development that is not yet fully tested that you would be able to provide. Would you be able to provide this along with any other recommendations?

Thank you!

Best Answer


  • rborgesrborges BostonMember

    Thank you for the reply!

  • thomasdelcourtthomasdelcourt bxlMember

    Hello, has there been any development regarding this type of analysis and this approach?

    Many labs I work with sequence panels of genes on tumour-only samples (at very high depth, eg. max 5000-20000 reads/base in targeted regions) without PoN. Are there guidelines/best practices for these kind of sequencings?

  • SheilaSheila Broad InstituteMember, Broadie admin
    edited August 2017


    Sorry for the delay. Have a look at this thread. We still do not recommend this or have Best Practices for it, but you can try running with only the tumor sample and a germline resource and a PoN. The germline resource will help filter out potential germline variants, and the PoN will help filter out artifacts.


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