How can I call somatic CNV in tumor and matched normal sample
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?
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Ram
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Smilesky •
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Smilesky •
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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.
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jared.andrews07
Disclaimer - I'm the author (of the command line wrapper not the R package facets): cnv_facets
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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.
Apologies! I’ve revised the question