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Processing Whole Exome samples with GATK4 Best practice workflow
What is the recommendation for processing WES samples with [PairedEndSingleSampleWf-fc-hg38.wdl] (https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/master/PairedEndSingleSampleWf-fc-hg38.wdl) regarding capture kit intervals file. Shell I use it instead recommended wgs_calling_regions.hg38.interval_list or apply capture kit intervals file to the final raw VCF file?