I have a fastq files from WGS but I want to subsample the reads and just runs it as WES, is there a way to do that?
Why not map as usual and find out which reads map to the exome?
Actually, because my pipeline is not optimized for WGS and it takes a lot of time to run the WGS so I want just subsample and map it to WES?
You don't know which reads come from exonic regions until you map them. As far as I know your only option would be to first map them all and then, if needed, extract the "exome" regions.