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missing FOXOG annotation for specific SNP variants in VCFs
We've run Mutect2 with OxoGReadCounts walker to obtain FOXOG annotation for somatic variants in VFCs. I know FOXOG annotation is only calculated for SNPs and when denominator (ALT_F1R2 + ALT_F2R1) is not null. However, I would like to know if there are some other conditions under the FOXOG annotation is not calculated since some SNPs were not annotated with FOXOG values. For instance:
GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1 0/0:710,18:1.351e-03:9:9:19396,531:347:358 0/1:602,5:4.393e-03:4:1:16497,153:288:305
Supposedly, this SNP variant has non-zero ALT_F1R2 and ALT_F2R1 annotated, so it should calculate FOXOG value but this value is not provided. Do you know why FOXOG is not calculated in these cases? I'm providing one additional example, just in case:
GT:AD:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1 0/0:818,19:0.012:12:7:24855,568:406:401 0/1:676,22:0.015:15:7:20245,679:359:307