Checking fastqc results from HiSeq 4000 run of PCR-free libraries and came across really high Sequence Duplication Levels.
Note: We were trying to sequence at high depth to detect somatic mutations (~240X).
Can't be PCR duplicates since these are PCR-free so it's a bit mysterious to me, though others might have ideas. Optical duplicates? Insufficient DNA in the sample? Should we be ok just removing duplicates or does this indicate something systemically wrong?