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
vidmap.json and what looks like a file for every chromosme with a
$ and contig boundaries specified in the BED file (e.g.
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
Thank you very much in advance for any help!