Can you please provide
a) GATK version used : 18.104.22.168
b) Exact GATK commands used: GATK Somatic CNV workflows, GATK Somatic SNV workflows
I am updating our lab's somatic characterization workflows to run on hg38-aligned data. I need an interval list (or BED file), defining the hg38 target intervals for the ICE exome capture kit used here at the Broad. The page describing the Broad Resource Bundle currently states:
In addition, we are currently transitioning to support the Grch38/hg38 reference build, but we have not yet generated all of the files necessary for all use cases (in particular we are still missing the Hg38 version of the Broad's exome intervals).
How do I obtain or generate an hg38 version of this exome interval list?
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