I can't find much info on this question online, so apologies if it is answered elsewhere. I'm working with whole exome seq data with the aim of identifying somatic variants. Using fastqc I can see adaptor in around 20% of reads by the end of the read (150bp PE). 

I always understood that adaptor trimming was routine in this situation but I have seen a few resources recommend against it, without providing any explanation as to why. Can anyone explain why it might be detrimental to trim adaptors prior to alignment?

Thank you
It is not detrimental to trim adapters. Reason some people choose not to do it is to save time, especially if you are aligning to a good reference (which you may be doing). Most aligners will soft-clip parts of read that do not align so in theory can take care of any adapter sequences that way. Personally I take the extra time to remove them so I no longer need to think about their presence for any downstream analysis.