How I can add the wheat reference genome database (I need to install 3D chromosome based database for the annotation of VCF file from 3D chromosome.
Since I referred the manual of snpEff at: http://snpeff.sourceforge.net/SnpEff_manual.html#run
and most of the examples given here based on human genome data.
So I couldn't even find a suitable wheat genome database (with 3D chromosome homeolog) at:
Kindly let me know concerning my request to implement the wheat 3D Homeolog databased at snpEff.
I used the model files with following script is working well:
time java -Xmx4g -jar snpEff.jar -v GRCh37.75 examples/test.chr22.vcf > test.chr22.ann.vcf