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GATK4 JointCalling WDL workflow interval lists

Dear Team,

I am working on GATK4 wdl joint calling workflow from below link

workflow using below intervals (unpadded and evaluation intervals). When I search resource bundle, I didn't found the related intervals.

"JointGenotyping.eval_interval_list": "/home/bshifaw/broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
"JointGenotyping.unpadded_intervals_file": "/home/bshifaw/broad-references/hg38/v0/hg38.even.handcurated.20k.intervals",

Could you please let me know how can I prepare interval list files for joint calling step?

Thanks In Advance
Fazulur Rehaman

Best Answer


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