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Why does Mutect2 @ GATK4 breaks everytime when running on single tumor mode?

Hi,

I have been using Mutect2 in tumor-normal mode, to create PON and now I am trying Mutect2 single tumor mode.
The program fails every time with sometimes 10 and sometimes 15 chromosomes, and is never completed. Do you have any idea what may be causing this. I am using exactly the script recommended here:

https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.0.0/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php

And, my data is mouse exome sequencing.
I have attached the end of the log file that describes the error.

Your help and views on this is highly appreciated. Thanks a lot.
Best Regards,
Yashna Paul

Best Answers

  • Accepted Answer

    Hi @shlee
    Thanks for your suggestions,
    I have tried several samples in tumor only mode, all fail at different genomic locations. These tumor bams work perfectly in tumor-normal pair mode. So there should not be a problem with the bam file. But I will still check them once again. Also, the best alternative is to then rum with a normal sample in a tumor-normal pairwise manner, as you suggested too.

    Thanks for your time.

Answers

  • yashnapaulyashnapaul Member
    Accepted Answer

    Hi @shlee
    Thanks for your suggestions,
    I have tried several samples in tumor only mode, all fail at different genomic locations. These tumor bams work perfectly in tumor-normal pair mode. So there should not be a problem with the bam file. But I will still check them once again. Also, the best alternative is to then rum with a normal sample in a tumor-normal pairwise manner, as you suggested too.

    Thanks for your time.

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