Hi, I'm trying to annotate variant calling with snpEff, using a reference genome (which I sequenced myself). I also have bed file with genes position corresponding with my reference genome.
I there a way to do so? I've tried to build database:
java -Xmx4g -jar snpEff.jar build -gtf22 -v q.fa
but got an error:
java.lang.RuntimeException: Property: 'q.fa.genome' not found
can snpEff accept a custom genome, or it must be from a public database?
also, is snpEff the proper tool for my need? any other suggestions? (organism is bacteria)
thanks a bunch