translocation detection question

[2nelly]

Hi all,

I am wondering...

how is it possible for tools like breakdancer and lumpy to detect translocations in a sample without using normal bam comparison? The reads aligned against the reference genome, however before the alignment we don t know the exact genomic position that every read came from. So, even if there is a translocation, the group of reads supporting a translocation will be aligned under the correct reference genome position.

Thank you in advance

[BnaT]

Hello,

BreakDancer, Lumpy and many others are based on the clustering of discordant signals from mapping to the reference genome. In the case of translocations, any read-pair supporting it might have a read1 mapped to chromosome A, whilst the read2 (or mate) is mapped to chromosome B. Moreover, Lumpy and in general split-read/assembly based algorithms refine the coordinates when the reads span across the breakpoint.

[2nelly]

BnaT, thank you for your answer.

Yes, I agree that using read-pair approach we can detect different alignment position of read 1 and read 2, but how do we know that translocation took place from chrA-->chrB and not from chrB-->chrA?