Dear Biostar Leaders,
We have a Paired End Sequencing Reads from Whole Exome Sequencing run generated on a cell line that is known to contain 15kb deletion on chrX. This 15kb region includes part of exon 4 of MECP2 gene. I have run Pindel and DELLY tools on it and this 15kb deletion is successfully detected by both the tools.
I am under the impression that Breakdancer can be applied only on Whole Genome Sequencing data, and not the Whole Exome data (WES). Please correct me if I am right or wrong.
Is it wise to run Breakdancer on a paired end WES data ?