I am trying to follow the example code at this site (http://snpeff.sourceforge.net/protocol.html) where snpEFF and GATK are linked together:
java -Xmx4g -jar snpEff.jar \ -v \ -o gatk \ GRCh37.71 \ protocols/ex1.vcf \ > protocols/ex1.eff.gatk.vcf
I have a data.vcf, data.fasta, data.fasta.fai, and data.gff3 file. I created a data.genome file by taking the first two columns of the data.fasta.fai file. The resulting data.genome file looks like:
So, I then tried to run the command on my files:
java -Xmx4g -jar snpEff.jar \ -v \ -o gatk \ data \ data.vcf \ > data.eff.gatk.vcf
But this led to an error: "java.lang.RuntimeException: Property: '/data.genome' not found"
My question is: Why can it not find the data.genome file? I checked my pathways. Is my data.genome file in the correct format? Additionally, I also read that I may need a code name for my data.genome file, but I cannot figure out how to do this?