"Copy Number Variation" detection in Tumor only sample
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7.0 years ago
Satish Gupta ▴ 40

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

Somatic Amplicon Panel Copy Number Variation • 3.9k views
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Have you processed a large number of normal samples with the same pipeline(s)? If not, you won't find any reliable method.

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

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7.0 years ago
Paul ★ 1.4k

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 :)

 

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