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How to prevent --germline-resource when running Mutect2 from removing germline variants

Hi,

I'm running Mutect2 in a tumor-only mode. I want to distinguish between likely germline and somatic mutations but I still want to keep both.

If I run the following command including --germline-resource I miss some variants that I can see are present with IGV and by running HaplotypeCaller. For example, if I run the following:

```
gatk Mutect2 -R $ref -L chr9:5450503-5470566 -I $outdir$outname"_split.bam" --germline-resource $afgnomad --panel-of-normals "/n/scratch2/vlachos/TCGA_Stomach/Normal/pon.vcf.gz" --af-of-alleles-not-in-resource 0 -tumor $outname --disable-optimizations --dont-trim-active-regions --bam-output $outdir$outname"mutect2.bam" -O $outdir$outname"different.vcf" 2>$outdir$outname.Mutect2.log
```
the output is:
```
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 0017fc99-38c2-4059-b34c-f9830a9c91ee
chr9 5468257 . G C . . DP=9;ECNT=1;POP_AF=0.251;P_GERMLINE=-5.977e-07;TLOD=18.99 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:4,5:0.556:2,1:2,4:40:135,145:60:16:0.535,0.525,0.556:0.024,0.027,0.949
```

When I exclude the --germline-resouce option:

```
gatk Mutect2 -R $ref -L chr9:5450503-5470566 -I $outdir$outname"_split.bam" --panel-of-normals "/n/scratch2/vlachos/TCGA_Stomach/Normal/pon.vcf.gz" -tumor $outname --disable-optimizations --dont-trim-active-regions --bam-output $outdir$outname"mutect2.bam" -O $outdir$outname"different.vcf" 2>$outdir$outname.Mutect2.log
```

the output includes a variant I can see exists in IGV. This variant has a population AF of around 0.5 so it makes sense it's excluded, but I still want to keep it, yet with a flag that it's likely germline.:

```
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 0017fc99-38c2-4059-b34c-f9830a9c91ee
chr9 5467955 . G A . . DP=16;ECNT=1;POP_AF=1.000e-03;P_GERMLINE=-2.169e-04;TLOD=46.63 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:2,12:0.812:2,2:0,10:40:655,198:60:12:0.838,0.848,0.857:0.033,0.022,0.945
chr9 5468257 . G C . . DP=9;ECNT=1;POP_AF=1.000e-03;P_GERMLINE=-2.169e-04;TLOD=18.99 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:4,5:0.556:2,1:2,4:40:135,145:60:16:0.535,0.525,0.556:0.024,0.027,0.949
```

Thanks!

Answers

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