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Mutect2: INFO field PON never reported

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Hi- I'm using Mutect2 from GenomeAnalysisTK-3.8-0-ge9d806836, everything looks good but I noticed that the vcf header of the output contains the INFO:

##INFO=<ID=PON,Number=1,Type=String,Description="Count from Panel of Normals">

I guess this field tells how many samples in the PON contain the variant, right? However, I never see the PON field ever used in the VCF records even if some variants are marked with the "panel_of_normals" filter, for example:

chr1    186341  .       T       G       .       panel_of_normals;t_lod_fstar    ECNT=1;HCNT=10;MAX_ED=.;MIN_ED=.;NLOD=14.65;TLOD=5.22   GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/1:50,3:0.057:2:1:0.667:1542,92:22:28  0/0:66,1:0.015:0:1:0.00:2068,29:41:25

Is this expected?

And possibly related... The description of the "panel_of_normals" filter says: Seen in at least 2 samples in the panel of normals. However, I prepared the PON using --minN 1 which should activate the panel_of_normals filter for just one normal found. Is this just an oversight in the description or am I missing something?

Here's the synopsis of the relevant commands I used:

java -Xmx5g -jar ~/applications/gatk/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar \
            -T MuTect2 \
            -R {params.ref} \
            -I:tumor {input.tumour} \
            -I:normal {input.normal} \
            --normal_panel {input.pon} \
            --dbsnp {params.dbsnp} \
            --cosmic {params.cosmic} \
            -L {params.chrom} \
            --min_base_quality_score 20 \
            --disable_auto_index_creation_and_locking_when_reading_rods \
            -o {output.vcf}

and for PON:

java -Xmx8g -jar ~/applications/gatk/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar \
             -T CombineVariants \
             -R {params.ref} \
             {params.variant_str} \
             -minN 1 \
             --setKey "null" \
             --filteredAreUncalled \
             --filteredrecordsmergetype KEEP_IF_ANY_UNFILTERED \
             -o pon/panelOfNormals.tmp.vcf

Thank you!


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