The highly unlikely situation happened.
My next generation seq. data have been aligned to bosTau7 build.
I am having troubles on building data set for that. And when I use lift up the vcf file with USCS bosTau7 build to UMD3.1 snpeff does not give me any annotation (the error different reference genome)
I downloaded gff file from the link below also tried ucsc to get gff file.
I have the bosTau7.fa
I am getting the error "java.lang.RuntimeException: Property: 'bosTau7.genome' not found"
# Bos_taurus genome: bosTaurus7
bosTau7.genome : Bos_taurus
java -jar snpEff.jar build -gff3 bosTau7 or java -jar snpEff.jar build bosTau7