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Why variant in germline-resource not filtered.
I have paired samples and I called them separately using following command, got a variant call in normal sample, not in tumor sample.
chr8:139165272 should be pre-filtered because it is in the germline-resource database. But how it was not filtered in the Mutect2 result?
normal sample: chr8 139165272 . TG CA . . DP=115;ECNT=2;MBQ=36,40;MFRL=218,208;MMQ=60,60;MPOS=43;POPAF=7.30;SAAF=0.323,0.333,0.354;SAPP=0.026,0.011,0.963;TLOD=147.15 GT:AD:AF:DP:F1R2:F2R1 0/1:73,40:0.356:113:30,21:43,19
~/gatktools/gatk-18.104.22.168/gatk Mutect2 \ -R ~/hg19/gatk_bundle/ucsc.hg19.fasta \ -I tumor.recalibrated.bam -tumor tumor \ -L chr8:139165272 --interval-padding 250 \ --germline-resource ~/af-only-gnomad.raw.sites.hg19.vcf.gz \ --tmp-dir tmpdir -O tmp.vcf