ref: Genes in gtf or gff format - genomewiki
1. Download your gene set of interest for hg19. For this example, I'll use the refGene table, but you can choose other gene sets, such as the knownGene table from the "UCSC Genes" track.
rsync -a -P rsync://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz ./
2. Unzip
gzip -d refGene.txt.gz
3. Remove the first "bin" column:
cut -f 2- refGene.txt > refGene.input
4. Convert to gtf:
genePredToGtf file refGene.input hg19refGene.gtf
5. Sort output by chromosome and coordinate
cat hg19refGene.gtf | sort -k1,1 -k4,4n > hg19refGene.gtf.sorted
