From your question it's pretty clear you're very new in bioinformatics. All I can offer is some buzzwords, and then there's a bit of reading required on your side.

What you have is the reference genome (fasta sequence) and its annotation (gff). You'll need some sequencing data, which typically come in compressed fastq format (like fastq.gz) file ending, which you can align to your reference genome to create a bam file. Popular short read aligners include bwa-mem and bowtie2, however, there's many more. These aligners create sam, or it's binary bam format. You can convert between both formats using samtools.