about multi-mapped reads and detection of chromosomal alterations

Question

[Bogdan]

Dear all,

a question about -- multi-mapped reads and -- not-mapped reads.

I received from our collaborators some BAM files for WGSA, where only the uniquely mapped PE reads were kept. In other words, if an end of the PE reads was not mapped, or it was mapped in multiple locations, these PE were discarded.

would you think that this process will affect our ability to detect DEL, DUP, INV, TRA ? thank you,

-- bogdan