I’ve been having following issues while building my reference genome in snpEff.
1. It is suggested to change the configuration file. No matter, where I’m putting the information about my reference genome in the configuration file, while running the java executable file, it can’t read.
2. In addition to the previous issue, the reference genome file provided in .fa format to build. But, it looks like while running the .jar file, it’s showing that “reference genome.fa.genome” is not found.
Does anyone build the reference genome using snpEff latest version or have idea about configuring file or reference file format issue?
I’ve looked at the instruction of snpEff and other related stuffs as well.
Download reference genome in .fa format and annotation file in .gff3 format from the following link: https://plants.ensembl.org/Zea_mays/Info/Index
Unzip both files and rename them accordingly:
Reference genome sequences.fa
Annotation file genes.gff
Remember to change the annotation file from .gff3 to .gff, otherwise snpEff wouldn’t be able to recognize it.
Make a new folder in inside your “snpEff” folder named “data”
Transfer those two files, sequences.fa and genes.gff, to the “data” folder.
Now, edit the snpEff.congif file. Add the following lines under ensemble release section.
# Zea Mays B73 genome, Version 4
Zea_Mays_B73v4.genome: Zea_Mays_B73v4
Now, go to the directory which contains snpEff.jar file, and run the following command.
java -jar snpEff.jar build -gff3 -v Zea_mays_B73v4
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