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"Copy Number Variation" detection in Tumor only sample

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
• 5,545 views • link
updated by Ram Ram • written by Satish Gupta • Satish Gupta

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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written by Devon Ryan Devon Ryan

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

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updated by Ram Ram • written by Danielk Danielk

1 answer

Hi Satish,

Did you try some good tools:

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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updated by Ram Ram • written by Paul Paul

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