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Update GCSTs for sumstats files and folders on FTP #1493

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eks-ebi opened this issue Nov 20, 2024 · 6 comments
Open

Update GCSTs for sumstats files and folders on FTP #1493

eks-ebi opened this issue Nov 20, 2024 · 6 comments
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@eks-ebi
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eks-ebi commented Nov 20, 2024

These two studies have had their GCSTs manually changed in the latest data release, but the FTP folders and the sumstats files are still named with the previous GCSTs.

  • previously GCST90454341 --> should be changed to GCST010098 - trait_description: Breast cancer
  • previously GCST90454343 --> should be changed to GCST010100 - trait_description: Breast cancer (triple negative or BRCA1-positive)

Tasks:

  • change sumstats filenames
  • move sumstats to correctly-named folders on FTP
  • change GCSTs wherever they appear in the YAMLs
@karatugo
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  • change sumstats filenames
  • move sumstats to correctly-named folders on FTP
  • change GCSTs wherever they appear in the YAMLs and md5sums
  • copy harmonised folder and do the above tasks for harmonised folder as well

@karatugo
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karatugo commented Dec 19, 2024

They should be available in the public FTP in a couple of days. (GCST010098 and GCST010100)

@sprintell
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@eks-ebi pls confirm done

@eks-ebi
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eks-ebi commented Jan 8, 2025

@karatugo It looks like there is a mistake here somewhere:
GCST010100 has the correct author notes and trait information in the YAML (Breast cancer (triple negative or BRCA1-positive)
but GCST010098 has the wrong metadata in the YAML (Protein S100-A10 levels) - I think this comes from a different publication

Can you see what could have happened?

@karatugo
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karatugo commented Jan 8, 2025

That particular issue with author notes being mixed up will be fixed after all yamls are generated. I'll check again in a couple of days.

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