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.
GATK18.104.22.168: steps, interval list, precision of the range (interval)
I'm still a little confuse about intervals. For example, personally I use the -L option in the following steps (-L):
BaseRecalibrator (-L): chr1... chrX, chrY ( =24contigns)
HaplotypeCaller (-L): 404 intervals*
GenomicsDBImport (-L): 404 intervals*
GenotypeGVCFs (-L): 404 intervals*
*is the whole genome without the gap-regions (reported in the UCSC browser)
I also work with cohort of WES which have different "exon targeted design".
My pipe is reliable/precise using the above intervals? or is better to use the regions/intervals of my "exon targeted designs"? If yes, in which step?