Testing out evolving small variant callers

broadinstitute / long-read-pipelines

Long read production pipelines

https://broadinstitute.github.io/long-read-pipelines/

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Testing out evolving small variant callers #181

Open SHuang-Broad opened 3 years ago

SHuang-Broad commented 3 years ago

Small variant callers with LRs are being pushed out/updated, so we need to keep track of major updates and new comers

List of interesting ones

New

[ ] dipcall
[ ] NanoCaller
[x] PEPPER (Maybe? considering it is much more than a variant caller)

Track major updates of

[x] DV
[x] drop Longshot
[x] Clair

kvg commented 3 years ago

I second this. I'll also suggest that we add noise-cancelling repeat finder (NCRF) to the mix.

SHuang-Broad commented 3 years ago

I think NCRF deserves a separate ticket tracking STR callers?

kvg commented 3 years ago

Yeah, I've looked into NCRF and am no longer sure it'll easily go into our workflows.

SHuang-Broad commented 2 years ago

Given that Clair3 doesn't seem to plan supporting CLR data (the claim there is interesting), we might be forced to evaluate NanoCaller, which calls InDels for CLR data.