SnpEff eff Error
My organism is Python_molurus_bivittatus-5.0.2 and I have one control and clown sample. I downloaded fna.gz and .gtf files from NCBI and made the database successfully on Galaxy server by using SnpEff build tool. After that when I tried to execute SnpEff eff to annotate variants, it produced the following errors:
What is the reason for it?
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anasjamshed
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It is not an error, is a warning, how does the output look like (if any)? Is your gtf sorted by coordinate?
the output look like this:
I did not sort the gtf file. Should I sort it by using bedtools sort?
That's just the header. The warning seems like an ordering problem to me, you should make a try.