In my WES data, I am trying to detect a single nucleotide insertion in tandem repeat region of variable length. But NGS reads cannot be mapped in this repeat, so I am not able to detect the insertion by WES data. Looking at the coverage across the gene, it suggests that the region is captured in our WES data which means the reads are there however cannot be analyzed due to mapping issue. So the question is what would be the best approach to detect this insertion using my WES data? I thought about few points that might complicate this analysis:
1- the increase in number of reads with insertions might be hidden within the noise.
2- it might be that the insertion creates a sequence that can be mapped to an alternative location, making it impossible to determine if the reads originate from the gene of interest, or from the other region.
3- the repeats are GC rich and the insertion converse a 7C stretch to an 8C length. Such insertions are common artifacts in NGS.
does anyone have a solution for that?