Hi all. I am doing an RNA Seq analysis for which I have created a few BAM files after alignment of the sequences to reference genome. I already have a .bed file which has some specific mutations from the same data(i.e a single file having mutations from all samples). I want to match those mutations to the particular sample (BAM) files to which they belong since the name assigned to mutations in bed files are different. I am trying to use bedtools intersect for this but it doesn't seem to be working properly. Could you suggest me any other way to do so or how to do it using bedtools itself. Thank you.
BAM files contain reads aligned to a reference sequence. Bed files contain regions defined by chromosome, start, and stop positions. Neither of these files contain called mutations. It sounds like you may need to use a variant caller to first call variants in your BAM files. Then, you can intersect the resulting VCF with your bed file to find mutations in the regions of interest.