Avatar

Genevieve Brandt

  • Total activity 232
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 1
  • Subscriptions 85

Activity overview

Latest activity by Genevieve Brandt
  • Avatar

    Genevieve Brandt commented,

    Another note - LiftoverVcf may be useful. https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard-

  • Avatar

    Genevieve Brandt commented,

    Hi Mike Zhu, this is an issue with dbSNP using a different naming convention (1,2,... instead of chr1,chr2,...). We are looking for a solution with our tool Funcotator at this link here: https://gi...

  • Avatar

    Genevieve Brandt commented,

    Hi Pedro Miguel Raposo: Please see this for more information about the Mutect2 algorithm: https://www.biorxiv.org/content/10.1101/861054v1 The GATK support team is focused on resolving questions ...

  • Avatar

    Genevieve Brandt commented,

    Hi neethukrishna Kausthubham, The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one,...

  • Avatar

    Genevieve Brandt commented,

    Hi Gaurav1983, please see this document for troubleshooting: https://gatk.broadinstitute.org/hc/en-us/articles/360043491652-When-HaplotypeCaller-and-Mutect2-do-not-call-an-expected-variant If that ...

  • Avatar

    Genevieve Brandt commented,

    Hi happyhihello, The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are build...

  • Avatar

    Genevieve Brandt commented,

    Has GATK worked for other commands for you? Also please run ValidateVariants to check if your VCF is in the correct format and post command and output. This also does not look like the entire stack...

  • Avatar

    Genevieve Brandt commented,

    Hi stanedav, thank you for posting about this. This looks like a bug and we have created an issue ticket to solve the problem. You can follow along here: https://github.com/broadinstitute/gatk/issu...

  • Avatar

    Genevieve Brandt commented,

    Hi wbsimey, you mentioned that you did this same workflow before with an older version of GATK. What version was that? Was it with the same data?  I also noticed that you are using SelectVariants t...

  • Avatar

    Genevieve Brandt commented,

    Hi Michael Franklin, I got more information about this tool in case you could get some runtime improvements. One question to consider, are you running this in a shared resources cluster with slow d...