Can someone explain what F1R2 and F2R1 counts mean?
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20 months ago
nickeener ▴ 50

I'm doing variant calling using GATK4's Mutect2 and trying to filter variants based on strand bias and other metrics and I feel like the F1R2 and F2R1 counts would be useful in this but I'm not entirely clear on what they mean. I understand that F1R2 is the number of first pair reads that mapped to the forward strand and the number of second pair reads that mapped to the reverse strand and F2R1 is just the opposite (correct me if I'm wrong please), but what does that actually mean biologically? What would good values for F1R2 and F2R1 look like? What would bad values look like?

Thanks!

variant calling mutect2 F1R2 F2R1 • 1.5k views
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