bed12

wget -O ~/bin/gtfToGenePred http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred
wget -O ~/bin/genePredToBed http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToBed
chmod +x ~/bin/genePredToBed
chmod +x ~/bin/gtfToGenePred


wget -q http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.refGene.gtf.gz

gtfToGenePred hg38.refGene.gtf.gz hg38.refGene.gp
genePredToBed hg38.refGene.gp tmp.bed
sort -k1,1 -k2,2n tmp.bed | bgzip -c > hg38.refGene.bed.gz
tabix --csi hg38.refGene.bed.gz

hg38.refGene.bed.gz can then be passed to jigv via --annotation hg38.refGene.bed.gz