I am trying to generate PON for WES samples following [GATK recommendations][1], they also have another explanation in this [Mutect2 article][2] but it's basically the same identical 3-steps procedure:

> ***step 1**. Run Mutect2 in tumor-only mode for each normal sample*:
`
gatk Mutect2 -R reference.fasta -I normal1.bam -max-mnp-distance 0 
-O normal1.vcf.gz
`

> ***step 2**. Create a GenomicsDB from the normal Mutect2 calls*:
`
gatk GenomicsDBImport -R reference.fasta -L intervals.interval_list 
        --genomicsdb-workspace-path pon_db 
        -V normal1.vcf.gz 
        -V normal2.vcf.gz 
        -V normal3.vcf.gz 
        -V ...
`

> ***step 3**. Combine the normal calls using CreateSomaticPanelOfNormals*:
`
gatk CreateSomaticPanelOfNormals -R reference.fasta       --germline-resource af-only-gnomad.vcf.gz 
      -V gendb://pon_db 
      -O pon.vcf.gz
`

I am using `gatk 4.1.7` (latest at the moment) but the output I got from step 2 (`GenomicsDBImport`) is a folder with some files in it, such as `vcfheader.vcf`, `vidmap.json` and what looks like a file for every chromosme with a `$` and contig boundaries specified in the BED file (e.g. `X$200786$155255277`).

If I try to pass this directory in the `-V` option of `CreateSomaticPanelOfNormals` (step 3 ) I got an error that the specified input is not a regular file, and GATK documentation confirms that `-V` is supposed to be a VCF file.

Does anybody, that maybe has generate PONs before or worked with this, knows what is the exact file output from step 2 that I am supposed to pass in step 3 `-V`?

Thank you very much in advance for any help!


  [1]: https://gatk.broadinstitute.org/hc/en-us/articles/360042479112-CreateSomaticPanelOfNormals-BETA-
  [2]: https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2
I've done this quite recently, with what I hope is the latest version.  
In my case I had to do this as below:

`-V gendb://pon_db`

the `gendb://` shouldn't be changed, and what follows is the path to the directory created by `GenomicsDBImport`