I'm trying to run cnv_germline_cohort_worflow in https://app.terra.bio/#workspaces/help-gatk/Germline-CNVs-GATK4/workflows workspace on my two cohorts, one in hg19 and another in hg38, and the input configuration preset in the workflow is only for running tutorial on chromosome 20, X, and Y in hg19, and the dashboard refers to GATK documentations for correct configuration. I have carefully read
this tutorial (https://gatk.broadinstitute.org/hc/en-us/articles/360035531152) and could learn what to use for some of the inputs, but there are still some inputs which require genome build specific files such as "contig_ploidy_priors" , "intervals", "mappability_track_bed /idx" , "segmental_duplication_track_bed/idx" , and some blacklist intervals that I have no clue where to get.
Is there an established Terra input configuration/resources for running the workflow on hg19 and hg38 germline WES dataset?
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