Question: CNV caller software
0
gravatar for Bogdan
3.2 years ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 wrote:

Dear all,

any suggestions regarding a good algorithm to use to call CNV (copy number variants) in the cancer genomes ? many thanks !

-- bogdan

cnv • 585 views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Bogdan580

Using what technology? exome-seq? (still an "open" problem, AFIAK) whole genome sequencing? arrays?

ADD REPLYlink written 3.2 years ago by Steve Lianoglou12k
Answer: CNV caller software
0
gravatar for Bogdan
3.2 years ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 wrote:

We have been using whole-genome sequencing ;)

ADD COMMENTlink written 3.2 years ago by Bogdan580

FYI: you should rather post this as a comment as opposed to an answer.

Another question is whether or not you have matched normal samples?

In any event, there are a large number of tools listed on this seqanswers page that you can thumb through.

ADD REPLYlink written 3.2 years ago by Steve Lianoglou12k

Thank you Steve. Yes, we have normal-tumor pairs. I looked on the page you sent me the link to, and of course, also in the literature, there are many algorithms. I was just looking for an algorithm that most of the community trusts and the results have been verified. Thank you ;;)

 

ADD REPLYlink written 3.2 years ago by Bogdan580
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 164 users visited in the last hour