The --finngen-annotation-version option is used to determine whether the finngen annotation supplied to the script is of the form used in the finngen annotation file r3_v0 and earlier, or the form used in r3_v1 and later. The former format is only used in R2 release (gs://finngen-production-library-green/R2/variant_annotation/R2_vep_annotated.tsv.gz), even the R3 release uses the current form (gs://finngen-production-library-green/R3/annotations/R3_annotated_variants_v1.gz). Therefore, there is not a lot to gain for having the option, as all subsequent analyses will use the newer format fg annotation files.
I suggest the option is deprecated, and an informative warning/error is raised if the file structure is the older one or invalid. This could be something like "Error: The file structure of the FinnGen annotation file is not recognized. Make sure the file is of correct form." This would have the advantage of simplifying the usage of the script.
At the very least, the newer format should be the default.
Lipastomies
commented
4 years ago
The
--finngen-annotation-versionoption is used to determine whether the finngen annotation supplied to the script is of the form used in the finngen annotation file r3_v0 and earlier, or the form used in r3_v1 and later. The former format is only used in R2 release (gs://finngen-production-library-green/R2/variant_annotation/R2_vep_annotated.tsv.gz), even the R3 release uses the current form (gs://finngen-production-library-green/R3/annotations/R3_annotated_variants_v1.gz). Therefore, there is not a lot to gain for having the option, as all subsequent analyses will use the newer format fg annotation files.I suggest the option is deprecated, and an informative warning/error is raised if the file structure is the older one or invalid. This could be something like "Error: The file structure of the FinnGen annotation file is not recognized. Make sure the file is of correct form." This would have the advantage of simplifying the usage of the script.
At the very least, the newer format should be the default.