How can I call somatic CNV in tumor and matched normal sample

Question

[Smilesky]

I am currently doing some exome analysis on Somatic samples where I am trying to do copy number analysis on tumor and matched normal samples (.bam) for. Can I know how to proceed with copy number analysis with with specific tools?

[jared.andrews07]

Depends on what the data actually is. Put a bit more effort into your question to provide the information we need to actually give an answer that might be correct.

[Smilesky]

Apologies! I’ve revised the question

Answer 1

[jared.andrews07]

I've always had decent results with cnvkit without too much messing around with parameters. Control-FREEC and ascat are other accessible options.

Read the documentation for examples, they are pretty simple to set up for your scenario.

Answer 2

[dariober]

Disclaimer - I'm the author (of the command line wrapper not the R package facets): cnv_facets