Hello,

It was my understanding that the `--max-population-af` filter removes germline variants present in the gnomAD germline resource with allele frequencies greater than 0.01 (the reported default value). However, in my resulting somatic_filtered.vcf.gz (from unpaired, tumor-only mode; see entire somatic workflow below), I am finding PASS variants that are present in the gnomAD resource with large allele frequencies -- chr5:157471682 is one example and has a reported allele frequency of 0.486. Could you please help me understand how this filter is working if it is not removing all variants that are present in the germline resource with AFs > 0.01?

Thanks in advance for your help,

Layne

REQUIRED for all errors and issues:
a) GATK version used: 4.2.2.0
b) Exact commands used:

1. Mutect2

    gatk --java-options '{java_opts}' Mutect2
      --native-pair-hmm-threads {threads}
      --reference {genome}
      --input {tumorbam}
      --panel-of-normals {pon}
      --germline-resource {afonly}
      --intervals targets.interval_list
      --f1r2-tar-gz f1r2.tar.gz  
      --output somatic.vcf.gz  
      --bam-output somatic.bam
      --tmp-dir /tmpdir

2. LearnReadOrientationModel

   gatk --java-options '{java_opts}' LearnReadOrientationModel
      --input f1r2.tar.gz
      --output read-orientation-model.tar.gz
      --tmp-dir /tmpdir

3. GetPileupSummaries

    gatk --java-options '{java_opts}' GetPileupSummaries
      --input {tumorbam}
      --variant {commonvcf}
      --intervals {commonvcf}
      --output pileup_summary_tumor.table
      --tmp-dir /tmpdir

4. CalculateContamination

    gatk --java-options '{java_opts}' CalculateContamination
      --input pileup_summary_tumor.table
      --output contamination_unpaired.table
      --tmp-dir /tmpdir

5. FilterMutectCalls

    gatk --java-options '{java_opts}' FilterMutectCalls
      --reference {genome}
      --contamination-table contamination_unpaired.table
      --orientation-bias-artifact-priors read-orientation-model.tar.gz
      --variant somatic.vcf.gz
      --output somatic_filtered.vcf.gz
      --tmp-dir /tmpdir