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 SnpEff.
- When I use the SnpEff download tool to download the SnpEff database for Mycobacterium_tuberculosis_h37rv, the tool runs successfully but outputs a file with only 2 lines. (SnpEff version number and Mycobacterium tuberculosis H37Rv).
I tried using the SnpEff build tool as well with the Genbank annotation file, however it results in the same 2 line output.
- Because of this problem, I directly downloaded the SnpEff database from SourceForge, and uploaded the file as a Snpeffdb to galaxy. This file however, shows as ‘unavailable’ in SnpEff eff. The issue might be with the metadata, which I am not able to edit manually and autodetect does not work.
As you can see I have tried all the approaches I can think of and nothing seems to work. I even used the galaxy.eu version. Please help, I am new to NGS analysis and will appreciate any guidance.