nf-core/hlatyping

Plans on class II?

Closed this issue · 7 comments

acrinklaw commented

Any plans on implementing tools that can perform class II typing as well?

christopher-mohr commented

Class II typing will be part of OptiType 2 which is currently under development. I would suggest to use it in this pipeline when its released.

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acrinklaw commented

Thanks for the response! I'm glad to hear there will be an OptiType 2. We currently have to rely on a combination of class I calls from OptiType and class II from other tools but the accuracy has been markedly lower for the non-OptiType results.

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gurpreet-bioinfo commented

Hi @acrinklaw Do you have any recommendation for class II tools for hlatyping?

acrinklaw commented

We use either PHLAT (which has low accuracy) or HLA-HD (which has significant runtime)

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christopher-mohr commented

I will close this for now but we will come back to this topic when OptiType 2 is available.

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