Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Variant calling on Tumor samples (exome) - HaplotypeCaller or UnifiedGenotyper?

Hi there,
According to your experience, what do you suggest for calling variants in tumor samples (exome) - HaplotypeCaller or UnifiedGenotyper? Have you seen any (major or minor) difference with both the callers on same exome tumor samples? What's your advice. Do you have any reference publication(s) where HaplotypeCaller is used on tumor samples?
Thanks
Raj

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Raj,

    We don't have any experience with calling variants on tumor samples; the HC and UG are both primarily designed for work on germline mutations, not somatic. Other users may be able to advise you better on this, but my recommendation would be to look into cancer-specific tools such as MuTect.

Sign In or Register to comment.