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GATK188.8.131.52: 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?