The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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?