Question: "Copy Number Variation" detection in Tumor only sample
0
gravatar for Satish Gupta
4.9 years ago by
Satish Gupta40
Warsaw, Poland
Satish Gupta40 wrote:

Hi Friends,

What is the best way to go for detecting copy number variation in Tumor only samples from NGS of Somatic cancer Amplicon panel from Illumina? I am able to do if I have a paired sample (Normal-Tumor).

I will be great for any suggestions or tools.

Regards,

Satish

ADD COMMENTlink modified 4.9 years ago by Paul1.3k • written 4.9 years ago by Satish Gupta40
1

Have you processed a large number of normal samples with the same pipeline(s)? If not, you won't find any reliable method.

ADD REPLYlink written 4.9 years ago by Devon Ryan92k

For WGS data, QDNAseq is actually very reliable in a tumor-only setting. No idea for amplicon data though. 

ADD REPLYlink written 4.9 years ago by Danielk570
1
gravatar for Paul
4.9 years ago by
Paul1.3k
European Union
Paul1.3k wrote:

Hi Satish,

did you try some good tools :

CNV-seq : http://www.biomedcentral.com/1471-2105/10/80

VarScan: http://varscan.sourceforge.net/copy-number-calling.html

Or maybe check this thread:

What Are The 'Copy Number Detection' Tools Out There For Exome Capture Ngs Data.

If you will find some good solution, please share it with us :)

 

ADD COMMENTlink written 4.9 years ago by Paul1.3k
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