about translocations in the cancer genomes

Question

[Bogdan]

Dear all,

I am asking for your a piece of info about the translocations and deletions that are called by various algorithms, such as DELLY, LUMPY, MANTA etc in the cancer genomes :

if there is a translocation between chrA:positionA and chrB:positionB, then shall we see in the output the following :

-- translocation chrA:posA-chrB:posB in the TRNSLOCATION file

-- deletion between chrA:posA -> end of the chromosome A

-- deletion between the beginning of chrB -> chrB:posB

is that is indeed the case, perhaps we can filter the more significant translocation by using the presence of corresponding deletions of the chromosome arms ? although of course, I understand that the other chromosome arms do not have to be lost by the cells.

thank you,

bogdan

[PoGibas]

How would you see deletion in chrA:posA if reads will be still coming from that place (yes, they are coming from a new position, but genetic material is not missing).

[vakul.mohanty]

Discordant reads should allow you to identify such modifications. Meerkat is a tools that identifies complex genomic rearrangements (http://compbio.med.harvard.edu/Meerkat/).