I am trying to get variants for a Candida glabrata isolate. I have already done mapping with Bowtie2 and variant calling with FreeBayes ( with the option for monoploid genome ). I couldn’t find and snpeff database for Candida glabrata so I created my own with .gbff file that I downladed from NCBI. After annotating variants with snpeff I get the ‘’ ERROR_CHROMOSOME_NOT_FOUND’’ error. I search galaxy.help for answers already but I found them complicated for me. I am probably doing something wrong but I couldn’t manage to find it.
I would be so grateful if anyone help me.
Note: I can share my history
Note2: I have also used lofreq for variant calling. ( At first I thought that was an issue because of FreeBayes )