Remove QUAL criterion from Low quality flag/Needs verification
Background
ELLA currently includes variant quality (originates from QUAL in VCF) as one of the criterion for flagging a variant as Q
(low quality) and giving a Needs verification
warning in the Quality section. The threshold is hard coded as <300. This has been for historical reasons, following the internal procedures.
The variant quality, however, is a poor metric to use for this purpose, mainly due to it being variant caller specific. In addition, in GATK it correlates with the total read depth, yielding very different values for single samples and trios (QD would be a better metric, but it's still caller specific).
Since we already use the FILTER column as a criterion, we should rather rely on that and let users add whatever criterion they want to flag to their pipelines.
Implementation
Remove the use of variant quality from low quality flagging (Q
indicator) and the Needs verification
warning.