Combining fastq/sorted sam files from same libraries run on HiSeq and NextSeq

Question

[senowinski]

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!

[Devon Ryan]

What do you want to do with them? Are you doing variant calling or something else?

[senowinski]

I want to call copy number variations on them. I should also add, this is low-pass sequencing combined depth of coverage will be 0.2X. thanks

Answer 1

[Devon Ryan]

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.