Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.
I want to use Mutect2 to call somatic mutations from cfDNA samples.
I found this post as also this (special use cases) and I would like to know if there are more details about how to set up Mutect2. Is there any special handle or set up or any recommendation in this case? I want to use it with Illumina NGS data, hot spot panel.
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