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VariantAnnotator and Mutect2
Dear Sheila, and Geraldine,
continuing our previous conversation about the fields in the VCF file produced by MUTECT2, please could you advise on why I see the following DIFFERENCES :
-- shall I run MUTECT2 with the options -A for FS, MQ, SOR, I am getting the following numerical values for a chr position :
FS=2.433; MQ=45.70; MQRankSum=-3.331 ; ReadPosRankSum=-0.654; SOR=1.489
-- shall I run MUTECT2 with NO -A options, but using VariantAnnotator on the VCF file in order to add FS, MQ, and SOR, the numerical values are :
FS=0.000; MQ=33.87; SOR=2.636;
the question would be of course, why these numerical values differ ? many thanks,