Hello, I am new to NGS and wanted to know which genes are present in my aligned file. I have performed BWA MEM to obtain a sam file and used picard to get a sorted.bam file. I also used bedtools to get a BED file and used its annotate utility to find the gene id or gene symbol for my reads. But it was only giving my the coverage. How do I get my gene symbols or gene ids using bedtools or any other tool?