How to take reads from WGS fastq files in order to map it with Exome?

Question

[jonessara770]

Hi

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?

Thanks Sara

[GenoMax]

Why not map as usual and find out which reads map to the exome?

[jonessara770]

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?

[bernatgel]

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.