REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:
Hi, I am using GATK v4.3.0 and the mutect2.wdl for whole genome analysis. I have found a wgs_calling_regions.hg38.interval_list from here:
Can you confirm that this is the file that we give to mutect2.wdl.inputs.json for the
"Mutect2.intervals": "File? (optional)" option???.
Can I also check, as there are 356 intervals in this file, is it optimum to give the scatter count as 356 (i.e. will the wdl split over the intervals listed or does it just split the total number of bases given in the interval list by the scatter count number?)
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