Large insertion sequence reconstruction from paired-end sequenced sample BAM files

Question

[Qboy]

Hi folks,

I am stuck with the sequence reconstruction of large insertions from my sample BAM files. They are up to 100 bp - 10K bp in size. I am not expecting the full reconstruction methods/tools, but if you know them, please be kind enough to share them in the comments. These insertions could be repetitive.

My samples are sequenced with the Paired-End strategy and are currently aligned to their corresponding RefSeqs.