Detect large deletions

[srr8623]

Hello,

Do you know if there are any bioinformatic tools to detect large deletions? We tried to detect >1 kb deletions from >10 Kb long PCR products; the long PCR products were fragmented to ~200 bp before adding adaptors.

Thanks!

[JamieHeather]

Might be a naive response, but if you're amplifying these wouldn't you see a >1kb deletion shift the band when you run it?

[srr8623]

Thank you for the feedback. Yes, you were right; we were able to see the shift of band based on gel electrophoresis of the long range PCR product. However, we now wish to find a bioinformatic tool that is able to call the large deletion from the NGS run results of the fragmented library for the long range PCR products.