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jmonlong / manu-vgsv

https://jmonlong.github.io/manu-vgsv/
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Edits and comments for results section #83

Closed jonassibbesen closed 5 years ago

jonassibbesen commented 5 years ago

Here are my edits and comments for the results section. The structure and flow is much better now compared to the first time I read the manuscript.

I noticed that both "call set" and "callset" is used in the manuscript (not only results section). I have not changed it since I did not know which spelling you prefer (I think both are correct). I have used callset in my edits.

eldariont commented 5 years ago

Excellent comments! You pointed me to a mistake I've made when switching from gold standard-based to sample graph-based evaluation. I think I should filter out all non-SV calls from the callsets before constructing the sample graphs in order to really compare SV genotyping performance and not general genotyping performance. I will fix this and clarify the manuscript accordingly.

eldariont commented 5 years ago

I thought that it's maybe better to put my changes on the yeast part into a separate PR. Therefore, I removed Jonas' two comments for now and will address them there. There is one remaining comment on Panel 1. Once this is addressed, we can probably merge this PR?!

glennhickey commented 5 years ago

Yeah, we want to push to get this posted to bioarxiv today, so let's merge what we can now. . no problem to pull out remaining comments into separate pr's or issues.

On Fri, May 24, 2019 at 10:27 AM David Heller notifications@github.com wrote:

I thought that it's maybe better to put my changes on the yeast part into a separate PR. Therefore, I removed Jonas' two comments for now and will address them there. There is one remaining comment on Panel 1. Once this is addressed, we can probably merge this PR?!

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jmonlong commented 5 years ago

I agree.

Fig1b should be fixed but the comment reappeared. I'll double-check and merge.