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Mutect2 not reporting QUAL values

I have some targeted panel data. I am using Mutect2 with the following command:

gatk Mutect2 --af-of-alleles-not-in-resource 0.0000025 --germline-resource af-only-gnomad.raw.sites.h19.vcf.gz -A BaseQualityRankSumTest -A ClippingRankSumTest -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest -A FisherStrand -A StrandOddsRatio -A InbreedingCoeff -L target.bed -I input.bam -R reference.fasta -bamout bamout.bam -tumor TUMOR --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter -O output.vcf.gz

I would like to perform hard filtering in these samples but I cannot obtain the QD value because QUAL value does not appear. I there anything I am missing?

Best Answer


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