Can I combine fastq/sorted sam files from the same samples and same libraries that were run on both the HiSeq and NextSeq? If it is absolutely fine (are there any pitfalls?), is there anything I should be weary of? Thanks!
If you're doing CNV detection then just merge the files and call it done. If you were doing something like variant detection or methylation sequencing then maybe you'd want to treat things a bit differently (due to the different error profile in the two aligners), but that's not needed in this case.