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EBISPOT / gwas-sumstats-harmoniser

GWAS Summary Statistics Data Harmonisation
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Improve tracking and versioning of harmonisation pipeline #28

Open aoifemcm opened 2 years ago

aoifemcm commented 2 years ago

Harmonised summary statistics lack tracking information, e.g. which version of the pipeline was used for harmonisation, which version of dbSNP is the data harmonised against.

All currently available harmonised data has used a 2018 version of dbSNP (@jdhayhurst or Yue can confirm). Will this be updated to a current dbSNP version when the optimised pipeline is implemented?

Yue's updated harmonisation pipeline includes a log file with some of this information.

ljwh2 commented 2 years ago

Discussed with James and Aoife. dbSNP comes from the Ensembl version which is defined in a config file. Decided to stick with the original dbSNP version in the first instance and discuss updating later on.