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Idea for the report table: A mini-plot that shows where Ns are in the assemblies #179
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:) good suggestion, actually we have something in this direction in place in covPipe, @MarieLataretu implemented a process that checks for important mutations and alerts when they are masked by N. For example, S:N501Y and when here an amplicon drop happens the user will get informed somehow. Am I right, @MarieLataretu ? |
status? @MarieLataretu @RaverJay @hoelzer |
No time, so i guess this remains in the idea stage :< |
You can specify a VCF file - the process checks if the position is N/low coverage and if the variation is found exactly as in the VCF or with another ALT. The output is a hand full of VCF files which are transformed into a table for the summary report in covpipe. I cloud plug this also into poreCov, but we still have to think about the output |
The topic came up again and we would like to add Nextclade's Also, we would like to have a closer look at the coverage of the spike. Do you think it's a good place for them, or should they better be published in the results? |
sounds good. so it will be in the final report then? |
I like the Spike-focused plots bc/ they are pretty helpful to briefly check for "masked" regions. Can we just have a "box" that one can extend to look at these plots? So the normal report does not get longer? |
+1 for the hide part |
I'll see what I can do :) You are thinking of the collapsibles we already have in the HTML table, right? |
Yeah, something like a button below the genome.coverage plots to expand all the spike zoomed plots |
Nice, I like! So with that it should be possible to get a quick idea if mutations are really missing/reverted for a certain lineage or just not called bc/ of low coverage in that region |
great love it
…On Wed, 30 Nov 2022 at 16:37, Martin Hölzer ***@***.***> wrote:
Nice, I like! So with that it should be possible to get a quick idea if
mutations are really missing/reverted for a certain lineage or just not
called bc/ of low coverage in that region
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Could also include warnings when N stretches are in important regions, e.g. the spike protein
As any mutations/deletions/insertions are just omitted when the corresponding region isn't covered enough, this might give a better overview what to expect.
Not sure on the details - and no idea where to find the time :D
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