My impression is that small InDel (a couple of bp) is identified through cigar string in BAM and typical CNV (at least thousands of bp) is detected through read depth.
What about InDel or CNV with size these them, say hundreds of bp? These CNV is too long to be covered by read and too short to be detected by statistically comparing the difference of read depth.
Do we have consensus that this kind of CNV is hard to detect? Or is there a common strategy of detection for them? Do we generally think them having impact on protein function (especially in oncology background) ?