To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Somatic Variant Calling with Tumor Samples Only

Hi,

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

Answers

  • rborgesrborges BostonMember

    Thank you for the reply!

  • 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, Moderator
    edited August 2017

    @thomasdelcourt
    Hi,

    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.

    -Sheila

Sign In or Register to comment.