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nf-core / hlatyping

Precision HLA typing from next-generation sequencing data
https://nf-co.re/hlatyping
MIT License
63 stars 30 forks source link

Plans on class II? #67

Closed acrinklaw closed 4 years ago

acrinklaw commented 5 years ago

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

apeltzer commented 5 years ago

@christopher-mohr are there?

christopher-mohr commented 5 years ago

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.

acrinklaw commented 5 years ago

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.

gurpreet-bioinfo commented 4 years ago

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

acrinklaw commented 4 years ago

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

gurpreet-bioinfo commented 4 years ago

Ok, thanks @acrinklaw !

christopher-mohr commented 4 years ago

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