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Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

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

    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.

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