I am using GenomicsDBImport, but since my input file is a file containing a list of file I don't know how to use this as input with GATK along with the
-V option. I've been looking for this everywhere, but I can't find this information in the GATK manual.
gvcf_list=gvcf.listaa java -jar gatk-package-126.96.36.199-local.jar GenomicsDBImport \ -R HG38/hs38.fa \ --genomicsdb-workspace-path /MY_DATABASE/$newdir \ -V $gvcf_list \ -L resources_broad_hg38_v0_wgs_calling_regions.hg38.interval_list
Thank you in advance