Set pre-defined configure files

EBISPOT / goci

GWAS Catalog Ontology and Curation Infrastructure

Apache License 2.0

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Set pre-defined configure files #1291

Closed jiyue1214 closed 1 month ago

jiyue1214 commented 2 months ago

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 commented 2 months ago

I have created pre-defined configuration for the BLOT-LMM, REGENIE and SNPtest.

METAL met some problems:

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

jiyue1214 commented 1 month ago

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.