Does anyone have a guide on how to decide on the VQSRTrancheSNP level to use? I have variants that are in the VQSRTrancheSNP99.80-99.90, VQSRTrancheSNP99.90to100.00, and VQSRTrancheSNP97.80to98.00.
I investigated one of the variants flagged with the VQSRTrancheSNP97.80to98.00 filter and seems to be a real variant.
Variant calling was completed by a different lab and we don’t have access to the plots from the GATK VQSRTranchSNP step.
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