Update status-db for bed files / capture kit

[hassanfa]

As a bioinfo/lab person, I want to be able to find the correct capture kit bed file and name to match bioinfo analysis and lims.

Problem: Names are complex and file names are not following same standard. The standard for these files are now ready: https://github.com/Clinical-Genomics/target_capture_bed/tree/file_name_convention#summary

There are two pieces that are important for lab: shortname and bioinfo: filename.

Expected outcome / suggested solution: Status-db to be update with correct meta data from https://github.com/Clinical-Genomics/target_capture_bed/tree/file_name_convention#summary

In https://clinical-api.scilifelab.se/admin/bed/ : Name --> ID or Shortname In https://clinical-api.scilifelab.se/admin/bedversion/ : Description to --> Shortname or ID

Possibly remove unnecessary info columns if no one is going to use them. These columns will be kept updated in https://github.com/Clinical-Genomics/target_capture_bed and it might be unnecessary to keep two locations updated. So maybe remove the following columns from status-db

Genes	Unique Transcripts	Transcripts With All Exons Covered	Transcripts With At Least One Exon Covered	Padding	Cosmic Snps	Non Genic Regions	Independent Segments

Questions: Q: Do shortnames need to be updated in lims? A: Yes. Q: . A: .

What needs to be done on the planning meeting:

• Estimate storypoints
• Remember to add label PBL Teamname

See https://github.com/Clinical-Genomics/development/blob/master/git/issue-reports.md for more!

[hassanfa]

@henrikstranneheim regarding in silico bed files for MIP, what else do you think would be needed to update in status-db?

[hassanfa]

@patrikgrenfeldt Here are some of the updates. Updating clinical_api would be much appreciated.

[hassanfa]

@patrikgrenfeldt any updates on this? What information do we need to proceed?

[annaengstrom]

@patrikgrenfeldt @hassanfa This is a very important issue for the cancer workflow, and should be done asap. I would actually argue that the gain is medium of high because using the incorrect bed file is not good at all...

[patrikgrenfeldt]

@patrikgrenfeldt Here are some of the updates. Updating clinical_api would be much appreciated.

Where is "here"? Is it the issue description? If we need to change the data I hope everyone can do that?

[hassanfa]

Wow... Come on dude, you sure know what " here " means 😟 and you sure know what I am refering to... Here as in this issue...

You were in the cancer meeting when we discussed updating bait set information ~two weeks ago. This issue is part of those discussions we had. Should I all the discussion we had here?

[patrikgrenfeldt]

You wanted to point my attention to this issue. OK, Thanks :)

So I'm a bit confused about what needs to be done. This data structure change described above I think I understand. I wonder if we are also talking about changing the actual data as well?, is that what causes the urgency??

[hassanfa]

This is hilarious. You second comment shows you clearly knew what might be needed to be done. Yet you asked what "here" means.

Anyway, to answer your qu, I suggest the following:

• review the meeting material
• talk to ALy to find out why and how this is urgent

This will tell how we want to sync statusdb and thereafter lims&bioinfo with proper baitset name and bed file.

[annaengstrom]

Bed - Name: is used for orders and is also visible on website and should not be changed

[annaengstrom]

Update of Bed Version in statusdb, taken from target_capture_bed:

short name

• [x] lymphomatic_2.1
  • [x] gi_cfdna_3.1
  • [x] gmck_solid_4.1
  • [x] gms_myeloid_5.1
  • [x] gms_myeloid_5.2
  • [x] lymphoma_6.1
  • [x] gms_lymphoid_7.1
  • [x] exome_8.1
  • [x] exome_refseq_9.1    

[patrikgrenfeldt]

Good work! Should we close the issue or is there something more to be done before we can think it is done done?

[annaengstrom]

Bra jobbat! Ska vi stänga ärendet eller är det något mer som ska göras innan vi kan anse att det är klart?

Jag tycker vi kan stänga detta ärende.

[patrikgrenfeldt]

resolved by #563