Dragen Germline Confidence scoring
In Franklin, each variant is given a confidence score which indicates the probability of the variant being a true or false variant. The score is based on several parameters of the variant calling and considers several biases and quality metrics.
The final confidence of the variant is based on the lowest confidence result from any of the rules below:
SNV and Indels
Failed
Variant caller filter - If it's not PASS in all callers then the variant confidence is Failed.
Low
If one or more of the conditions are met then the confidence is low:
Quality - below 10.
Failed in gnomAd - if the variant has a failed flag in gnomAd then the variant confidence is reduced to Low.
Homopolymer - if a variant has low AB (below 0.25) and it's a one-base indel whose deleted/inserted base is in a region of a homopolymer of the same base (10 and above bases in sequence) then the variant confidence is reduced to Low.
Medium
If one or more of the conditions is met and none of the Low conditions is met then the confidence is medium:
Quality - between 10-20
High
If all conditions are met and none of the Low/Medium conditions are met then the confidence is high:
Quality - above 20.
CNV
Failed
Variant caller filter - If it's not PASS in all callers then the variant confidence is Failed.
Low
If one or more of the conditions are met then the confidence is low:
Quality - below 100.
Medium
If one or more of the conditions is met and none of the Low conditions is met then the confidence is medium:
Quality - between 100-120
High
If all conditions are met and none of the Low/Medium conditions are met then the confidence is high:
Quality - above 120.