Inquiry about integrating Octopus variant caller into Sarek

[alkhatib93]

Description of feature

Hello,

We’ve recently been benchmarking Sarek using DeepVariant on GIAB samples and observed a relatively higher number of false positives compared to the GIAB benchmark VCF.

I came across literature and community discussions suggesting that Octopus performs particularly well in reducing false positives while maintaining strong sensitivity. Given that Sarek already supports multiple variant callers (GATK, DeepVariant, Strelka2, FreeBayes, etc.), I wanted to ask if there are any plans to integrate Octopus into Sarek in upcoming releases, or if there have been previous considerations or discussions around it.

Best regards,
Mohammed Alkhatib

[FriederikeHanssen]

Looks like we looked at it at some point but the installation was not trivial: #95 (comment) . If this has changed, we'd welcome a contribution