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Mutect2: INFO field PON never reported

darioberdariober Cambridge UKMember

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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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @dariober
    Hi,

    It sounds like those are bugs in GATK3 MuTect2. Since there will be no more development on that, can you try with GATK4 beta 6?

    It looks like the PON annotation has been replace by IN_PON which tells you if the site is present in the PoN. In the new workflow (which you can learn more about in the presentations section), the tool automatically considers a site IN_PON if it is present in two or more samples. However, you can control the filtering with FilterMutectCalls.

    -Sheila

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