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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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misleading mosaic tag at case level #1718

Open 4WGH opened 4 years ago

4WGH commented 4 years ago

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the mutation is true positive, but it is NOT a mosaic. Can the tag be moved in another position? so it dones not seams it is a true positive?

As it is a de novo variant; I've checked the parental sample reads and noted this on the mosaic tag. see below

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northwestwitch commented 4 years ago

An option would be to remove completely the mosaic tag from there, because move it around I don't think it's the case

4WGH commented 4 years ago

For me it is OK. But better to check with Danielmailto:daniel.nilsson@scilifelab.se who put it in. Maybe there was a reason/need he though about :)

Från: Chiara Rasi notifications@github.com Skickat: den 18 februari 2020 15:38 Till: Clinical-Genomics/scout scout@noreply.github.com Kopia: Michela Barbaro michela.barbaro@sll.se; Author author@noreply.github.com Ämne: Re: [Clinical-Genomics/scout] misleading mosaic tag at case level (#1718)

An option would be to remove completely the mosaic tag from there, because move it around I don't think it's the case

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dnil commented 4 years ago

Well, @4WGH was the one who requested the “not observed to be mosaic” option to the “mosaic” tag, and is likely the most avid user of it, so her opinion is vital. 😄

Removing it is quite fine with me, but if so preferably just that latest option value. The tag on the pinned variant is not exactly vital, but does serve a purpose for actual mosaic variants.

The slightly more complicated, but more functional way would be to hide the pinned mosaic badge if the mosaic tag is None or Not observed in parents. Or show the mosaic tag contents in a tooltip.

northwestwitch commented 4 years ago

I propose that since she was the one to propose the "not observed to be mosaic" she'll continue seeing it while we make it disappear for all the other users! 🤣

4WGH commented 4 years ago

"The slightly more complicated, but more functional way would be to hide the pinned mosaic badge if the mosaic tag is None or Not observed in parents. "

sort of agree, even if the opsiton None or Not observed in parents ar not available.

If the pinned mosaic badge doent not appear if the tag: "not evident in parental reads" is selected. would be perfect.

I still thin that that badgt shout not be before the "validation choide" as that refer to the variant validatiom that not necessarely confirm a mosaicism.

possible suggestions:

  1. just move it bild

2: Had a tag also for confirmation of mosaicism (advanced, more for future?) maibe other group could appreciate it ? bild

  1. the badge could be changed to "mosaicims?" if the tag "suspect in is choosen".
northwestwitch commented 4 years ago

I honestly don't like much the idea of showing or not showing the mosaic tag after checking which mosaic tags are selected. For code (and conceptual) simplicity I think that if any mosaic option is selected then the mosaic tag should be shown. An alternative would be to hide the mosaic tag regardless of which mosaic option is selected.

I'd either show it or hide it regardless of the selected options.

An alternative would be to completely remove the "not observed in parents" from the mosaic tag (which I think makes more sense) and put it somewhere else. Could be a comment as well.

4WGH commented 4 years ago

no no no please do not remove the "not observed in parents" that is the mostly used tag that i wished to have since a loooooong time.

That is extremely important for all de novo mutations when there is a trio analysis.

4WGH commented 4 years ago

I've discussed with Nicole, she also think the badge is misleading. Better to remove it then.

4WGH commented 4 years ago

Regarding the idea of showing or not showing the mosaic tag after checking which mosaic tags are selected I think it is a very cool option (@dnil )

I can understand if problematic for coding, so I'm not pushing for it.