[galaxy-user] How to extract geneID from pileup file?

Dear galaxy-users, I am working on a project to identify and genotype SNPs in targeted genes. I did some analysis using Galaxy. First, mapping to the genome with Bowtie. Second, identify SNPs using MPileup in SAMtools. When I got the pileup file, the SNP information is in which chromosome and what position. I would like to focus on the SNPs within genes. How could I extract the SNP information for each genes (SNP position, coverage)? Is there a tool in Galaxy to fulfill this? Any help is highly appreciated! Best wishes, Yan