Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?