[User Story] Merge VarDict and TNscope results

[mathiasbio]

Need

As a clinician I want as many true variant calls as possible while avoiding false positives. VarDict has proven to be unreliable in both performance (crashing due to memory issues) and in terms of variant calling (#1396) and it was intended initially to replace it with TNscope for release 16 (#1428) however while this replacement showed improvements in all aspects of the validation criteria (#1429), while manually inspecting the unique calls from VarDict that were missing in TNscope there were evidences of inconsistencies in TNscope as well. Bug reports have been made to Sentieon regarding these issues.

Suggested approach

While waiting for TNscope issues to be resolved by Sentieon in upcoming releases, and perhaps adding additional SNV callers to replace VarDict, we can continue to use VarDict and try to shore up its weaknesses by adding TNscope.

Considered alternatives

Replace VarDict with TNscope, didn't feel safe to implement with current issues in TNscope.

Deviation

No response

System requirements assessed

• Yes, I have reviewed the system requirements

Requirements affected by this story

No response

Risk assessment needed

• Needed
• Not needed

Risk assessment

No response

SOUPs

No response

Can be closed when

#1475

Blockers

No response

Anything else?

No response