about translocations in the cancer genomes
0
1
Entering edit mode
8.1 years ago
Bogdan ★ 1.4k

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

SNP • 2.0k views
ADD COMMENT
0
Entering edit mode

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).

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 999 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6