The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Why does Mutect2 @ GATK4 breaks everytime when running on single tumor mode?
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:
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.