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Export managed variants from scout #2697

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jemten opened this issue Nov 20, 2023 · 0 comments · Fixed by #2750
Closed

Export managed variants from scout #2697

jemten opened this issue Nov 20, 2023 · 0 comments · Fixed by #2750
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@jemten
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jemten commented Nov 20, 2023

Description

In scout the customer can maintain a list of managed variants which should never be filtered away and always be uploaded to scout. MIP and the coming raredisease pipeline needs to have this file presented before each start in order to have an up to date whitelist to use, similar to how the gene panels are exported and used.

Suggested solution

Add the call scout export managed --build <genome_build>, possibly with the flag --collaborator <cust_NR>, to cg

This can be closed when

When the command has been added and the file is presented to the pipeline.

Blocked by

Clinical-Genomics/MIP#2062

@henrikstranneheim henrikstranneheim linked a pull request Dec 7, 2023 that will close this issue
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@henrikstranneheim henrikstranneheim self-assigned this Dec 8, 2023
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