Can you please provide
a) GATK version used gatk 184.108.40.206
b) Exact GATK commands used
c) The entire error log if applicable.
Can you provide a pipeline command for cancer panel target sequencing (with cancer-only-fastq and interval file, from bwa, markduplicate, BQSR, Mutect2?) to call somatic variants as I feel the evolving of gatk version makes me very confused. Many thanks.
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