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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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MT (eklipse) display in Scout with RareDisease pipeline #4703

Closed Lucpen closed 2 months ago

Lucpen commented 2 months ago

Is your feature request related to a problem in the current program to new available techology or software? Please describe and add links/citations if appropriate. It would be great to have access to the eklipse output on a sample by sample basis. It consist of an image and 2 tables per sample. It would be great to be able to download the tables so that they can be placed in LIMS if relevant to the case

Describe the solution you'd like Be able to see and downlaod eklipse results sample by sample

Describe alternatives you've considered A clear and concise description of any alternative solutions or features you've considered.

Additional context Add any other context or screenshots about the feature request here.

dnil commented 2 months ago

Please provide an example of the tables, and we will see what we can do. In the WGS rare disease pipelines we started off with just producing the images. These can already be loaded if you just provide the paths in the load config!

Lucpen commented 2 months ago

Here are the file name and headers:

dnil commented 2 months ago

It kind of looks like a very early stage of building towards an SV caller for MT? Wouldn't it be more relevant to get back when they produce VCFs? Did they resume work on the tool by the way - it kind of paused there after some student left?

dnil commented 2 months ago

I would prefer closing this as wont fix. The data in the first csv could be annotated a little bit better and then made VCF instead. Then it would both parse automagically in scout, and also could be combined with the other sv callers, local frequency collected in loqus etc. And if all that happens is someone taking a cursory look, then the images should be enough? But again, please explain the use cases, and we could work with what is given. It further complicates things that the tool is unmaintained. I am not happy about providing that to the clinic side.

dnil commented 2 months ago

Oh, and to be clear, eKLIPse images can and is already shown in scout per sample from some pipelines, as general images on the case.