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openvax / topiary

Predict mutated T-cell epitopes from sequencing data
Apache License 2.0
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Don't seem to be filtering stop-gain variants #48

Open iskandr opened 8 years ago

iskandr commented 8 years ago

Noticed some variants such as "p.W146*" in @timodonnell's neoepitope predictions.

iskandr commented 8 years ago

@timodonnell @arahuja @tavinathanson Should we use a default of only_novel_epitopes = True?

(https://github.com/hammerlab/topiary/blob/master/topiary/predict_epitopes.py#L54)

tavinathanson commented 8 years ago

I think the primary goal of topiary is only_novel_epitopes, so I think it's fairly confusing to default to False?

timodonnell commented 8 years ago

Yes, definitely agree we should default that to true

iskandr commented 8 years ago

Remind me, did we ever fix this?