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Set pre-defined configure files
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
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
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.