GATK version used: gatk4-18.104.22.168-0/gatk-package-22.214.171.124
Dear GATK experts,
I am trying to concatenate multiple GVCFs (all same samples, different genomic intervals) but having the following error:
A USER ERROR has occurred: Couldn't read file file:///mnt/shared/scratch/ssharma/private/tsb_spet/intervalwiseCombinedGvcfs.spet.tsb/spet.tsb.SPET.final.variants.g.vcf.gz
I have checked all input files are fine and in the correct genomic order.
If possible a prompt reply would be helpful even just to clarify whether GatherVcfs can also be used to combine GVCFs or this tool is only for VCFs.
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