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Seems Not The Right Genotype of My variants
Hello this is my GT:AD:DP:GQ:PL information of my variants : 0/1:4,42:46:11:1429,0,11 . It seems that "1/1" might the best genotype of my variant, can anybody tell me the reason.
This is my command: genotyping_mode DISCOVERY --emitRefConfidence GVCF -stand_call_conf 10