We use the following interval lists for our Agilent/ICE WES samples (paths are on Google Cloud Storage):
AGILENT target intervals (hg19):
gs://firecloud-tcga-open-access/tutorial/reference/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list
ICE target intervals (hg19):
gs://firecloud-tcga-open-access/tutorial/reference/whole_exome_illumina_coding_v1_plus_10bp_padding_minus_mito.Homo_sapiens_assembly19.targets.interval_list
