Summary statistics file formatter

[jdhayhurst]

• Plink2.0 has an option to output files in the gwas-ssf standard format
• Not everyone is using plink to generate their files for submission to the GWAS Catalog.
• For users not using plink, how do they generate their gwas-ssf files?
• What can we do to make it easier for users to generate gwas-ssf?
• Software to convert existing tabular data to gwas-ssf
• What type of user - CLI or GUI?
• Acceptable input formats?
• Limitations? Resource considerations
• Is this just a typical ETL problem?
• Existing generic tools:
  • petl python package and cli
  • sumstats formatter python package and cli

[jdhayhurst]

1. assess users' (curators) requirements
2. make more user friendly e.g. interactive cli
3. sequence of operations like petl exec chaining idea (handled by the above)
4. deprecate sum-stats-formatter and merge into: https://github.com/EBISPOT/gwas-sumstats-tools