The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
Where is "known_indels_sites_VCFs" defined?
Dear GATK team,
I have been translating your wdl files into shell scripts to map them better to the scheduler on our Linux cluster (shell scripts are not already available anywhere, are they?).
At some point in the PairedEndSingleSampleWf.wdl you reference known_indels_sites_VCFs, I thought this array would be defined in JointGenotypingWf.hg38.inputs.json however the name known_indels_sites_VCFs is not specifically mentioned there and the files listed under "##_COMMENT4": "KNOWN SITES RESOURCES" are not only known indel sites, but also snps. So my question is: Is known_indels_sites_VCFs this entire list or some subset of said list? If it is a subset, where is it defined?