I have run CONTRA tool and got the following output.

Command- ./contra.py -t /home/s/agilent_human_region.hg19.bed -s /home/s/Projects/Tumor.bam -c /home/s/Projects/Normal.bam -f /home/s/hg19.fa -o /home/s/Contra_output

Output-

Targeted.Region.ID Exon.Number Gene.Sym Chr OriStCoordinate OriEndCoordinate 73902 0 unknown chr15 21051082 21051202 223270 0 unknown chr8 143592311 143592466

I got the Gene.symbol column as unknown thus not able to identify the gene name.Why is that the gene.symbol is unknown ? Where did I go wrong ?