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.