this is a very general question. You need to start with the basic NGS analysis, like Quality control (FASTQC), optional trimming and mapping (bowite2, bwa). If you have mapped reads you can convert your BAM file (the mapped reads) to BED file (region) file. This file can be intersected with know regions etc.
I know this answer is also very general but it's quite easy if you search for the keywords mentioned in this text.