CallOverlappingConsensusBases vs "consensus-call-overlapping-bases" in CallDuplexConsensusReads

[gevro]

Hi,
What is the difference between:
CallOverlappingConsensusBases tool
vs
"consensus-call-overlapping-bases" in CallDuplexConsensusReads tool
?

The former tool has two options: agreement-strategy and disagreement-strategy

But these options are not available in the CallDuplexConsensusReads tool.

What strategy is used by CallDuplexConsensusReads "consensus-call-overlapping-bases" option? And is there a way to change options there?

Also, I'm assuming that running both of these in the pipeline is not recommended?

Thanks

[tobyaicher]

Hi,

I wanted to follow-up on this issue as I am also interested in the answer.

Thanks

[nh13]

The CallDuplexConsensusReads tools use the Consensus agreement and disagreement strategies. We do not expose both as command line options to the tool, like we do for CallOverlappingConsensusBases .

Running both of these is not recommended. Pick one, and only CallOverlappingConsensusBases if you want to explore different agreement and disagreement strategies.

If you want a different strategy for CallDuplexConsensusReads, feel reach out and we may be able to help if you'd be willing to provide some motivating examples.

Also, feel free to re-open if this doesn't answer the question.