Hi, I have been trying to run SnpEff in Galaxy, but have been facing a number of issues that I am not sure how to resolve. Background: I am analysis different strains of Mycobacterium tuberculosis. I have created a vcf file, and would now like to see the effects of my variants, hence I am using Snp…

Hmm, from your description (which is very detailed BTW - thanks for that!) there does not seem to be anything wrong here. Those two lines of output are how Galaxy presents the newly downloaded genome to you. After all, SnpEff genome files are kept in a binary format and there is not really a more he…

Thank you so much for your prompt response. It worked!

Linked Q&A: How to add Triticum aestivum snpEff4.3 genome database or appropriate wheat genome database in Galaxy for VCF annotation?

Galaxy Community Help

SnpEff errors while trying to run the tool

usegalaxy.org support

vcf-filter, snpeff

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