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again about the AD field
Dear Sheila, and Geraldine,
also please could you advise on understanding the data in the VCF files of NORMAL and TUMOR for the variant at this position (from MUTECT2) : chr21 46689620 : especially the FS, SOR, and the AD.
chr21 46689620 . G A . PASS BaseCounts=7,0,27,0;ECNT=1;FS=0.000;HCNT=1;HRun=4;MAX_ED=.;MIN_ED=.;MQ=33.87;NLOD=6.16;SOR=2.636;TLOD=10.90;VariantType=SNP GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:20,6:0.240:5:1:0.833:408,145:8:12 0/0:21,0:0.00:0:0:.:435,0:11:10
I have also attached the images from samtools tview - for NORMAL and TUMOR : will describe the questions and the calculations below