EBISPOT / gwas-summary-statistics-standard

Documentation on new GWAS Summary Statistics Standard
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Effect size variables #16

Open ramiromagno opened 1 year ago

ramiromagno commented 1 year ago

Currently the standard allows for three alternative column names to represent the effect size:

This is a mandatory field. These alternatives, particularly when one of them is mandatory, makes the parsing more difficult.

I would prefer to have one column named effect_size, and then have the metadata explain which of the three cases is it.

jdhayhurst commented 1 year ago

Hi Ramiro, it's good point and one we have discussed. The main thing is that the column index is consistent for effect size. Second, we originally had effect_size as the label, but this would force users to read the metadata file to correctly interpret the data. Given that the metadata is in a separate file (an issue discussed elsewhere!), this was deemed potentially laborious so we've put that metadata into the column header itself.