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Set pre-defined configure files

Open jiyue1214 opened this issue 10 months ago • 2 comments

To make it more convenient for users who have generated their results using popular tools, we should provide pre-prepared configuration files that they can directly apply to their data.

  • [x] change gwas-sumstat-tools format to recognise the software name
  • [x] Prepare the pre-defined configure files for general tools
  • [x] Update the UI and code to allow the user to select the analysis software

Need to prepare pre-defined configure files for

  • [x] SNPtest
  • [x] REGENIE
  • [x] BOLT-LMM
  • [ ] METAL

jiyue1214 avatar Apr 16 '24 16:04 jiyue1214

I have created pre-defined configuration for the BLOT-LMM, REGENIE and SNPtest. Screenshot 2024-04-30 at 22.33.33.png

METAL met some problems:

  1. METAL can generate two outputs, one is Effect(beta) + stdErr and other other is z-score + weight(sample number)
  2. METAL has markerID column, which can be rsid or variant_id. If it is rsid, there will be no chr and pos info

jiyue1214 avatar Apr 30 '24 21:04 jiyue1214

I have created the pre-defined configuration for SNPtest, REGENIE, BOLT-LMM and SAIGE. But not for the METAL because it does not match gwas-ssf requirements and there are two different outputs. This ticket is done.

jiyue1214 avatar May 14 '24 19:05 jiyue1214