Regarding SNP eff

hello galaxy community,
I require assistance with SNP Eff analysis for my Candida species, which isn’t on the pre-configured list. While I’ve attempted creating a custom database using GenBank GFF/GBFF/GTF formats, it’s encountering issues. I appreciate any guidance troubleshooting or alternative approaches for annotating my variants.

Hi @Muhammad_Rizwan

The SnpEff build tool has help directly from the tool author on the form – scroll down to see it. If one sort of input is failing (and you confirmed the format), you can try another. They also listed out some common gotchas and what to do about them. The logs for this tool also tend to be informative, so be sure to review those.

Reference annotation data comes in several formats – and data providers produce hybrids! But those can usually be standardized. This forum has a lot of help around that. I’ve added some tags to your post that will find them. These are two of the primary FAQs we host. The second is for DE analysis, but the “rules” about how different inputs (eg reference genome + reference annotation) work together is the same for all tools.