Issues while trying to create my own PON (Panel Of Normals) with GATK

Question

[Samuel]

Hey guys,

My goal is to filter my mutect2 generated VCFs (somatics). I am trying to create a PON (Panel Of Normals), so I can use FilterMutectCalls with my PON.

This command doesn't work :

gatk CreateSomaticPanelOfNormals \
     --vcfs KTN302-2_mutect_PON.vcf.gz \
     --vcfs KTN102-b.hg38_multianno.vcf.gz \
     -O two_samples_pon.vcf.gz

(i get : vcfs is not a recognized option)

So I am trying to use this instead:

gatk CreateSomaticPanelOfNormals \
     --variant KTN302-2_mutect_PON.vcf.gz \
     --variant KTN102-b.hg38_multianno.vcf.gz \
     -O two_samples_pon.vcf.gz

But i get the error : Argument '[V, variant]' cannot be specified more than once.

So I did a lot of research and found out a possible solution at GATK Mutect2 Panel-Of-Normals generation

It is an advise to use GenomicsDBImport before employing CreateSomaticPanelOfNormals :

gatk GenomicsDBImport -R /home/sbesseau/scratch/LOTUS/genome.fa -L test.intervals.list\
       --genomicsdb-workspace-path pon_db \
       -V KTN302-2_mutect_PON.vcf.gz \
       -V KTN102-b.hg38_multianno.vcf.gz 

I produced the intervals.list by myself (chr1 ... chrM), but I get the following error running GenomicsDBImport: GenomicsDBImport does not support GVCFs with MNPs.

I saw this issue was solved with haplotypecaller adding the option --max-mnp-distance 0. But this option doesn't existe with GenomicsDBImport , so I am stuck. Any idea?

I use gatk 4.1.2.0.

Thank you very much