Is it okay to map reads from WES designed for GRCh37 to GRCh38?

Question

[samuelandjw]

Suppose I have WES reads (in fastq format), and the capture regions are based on GRCh37 coordinate. Can I map the WES reads using bwa to GRCh38 coordinate? If not, what problems would arise?

[Pierre Lindenbaum]

there won't be any problem; The reads don't "know" where they've been designed. The only thing to do is to liftover your bed capture. May be you'll lost a few regions in the process.