GATK MUTECT2

Question

[Hyeong Seok]

I am trying to make PON for WES samples (tumor-blood matched sample) by following GATK recommendations, there is another method with 3-step procedures:

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

-> I can get vcf.gz files

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 ...

-> from step 2, which is the output file???, is there any default interval_list files?

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

-> from step 3, where can I get --germline-resource ????, and -V gendb://pon_db?? can I use it at it is?

I have no idea about this command... for each step, which input file do I need and which is the output??? Let me know...

Thank you very much in advance for any help!