"Copy Number Variation" detection in Tumor only sample

Question

[Satish Gupta]

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

[Devon Ryan]

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

[Danielk]

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

Answer 1

[Paul]

Hi Satish,

Did you try some good tools:

• CNV-seq
• VarScan

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 :)