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snakemake / snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see
https://snakemake-wrappers.readthedocs.io
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Varscan/Snpeff wrappers are incompatible - please add warning to documentation #275

Open moldach opened 3 years ago

moldach commented 3 years ago

When running the two snakemake wrappers Varscan -> SnpEff in succession there is an error thrown https://github.com/pcingola/SnpEff/issues/267#issuecomment-736928876

This does not happen when feeding Varscan to the VEP annotation tool.

This should be mentioned on the docs: https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/varscan.html

gabrielet commented 8 months ago

i write, here too (other post here). any news on the topic?

fgvieira commented 8 months ago

I am not familiar with Varscan2 output but, if the ID field is missing, then it seems this is a Varscan2 issue. If you want to add a disclaimer to the wrapper, you can make a PR and I will merge it.