Hello! I have tumor only samples (.bam) for copy number analysis and no normal samples. Can I know how to proceed with copy number analysis with tumor samples with specific tools?
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written
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Saurabh •
4 answers
Take a look at sarek: https://nf-co.re/sarek/3.4.0 I believe it supports tumor-only CNV calling
You can compare to a public panel-of-normal or do a relative CNVs if you have different tumor-condition samples (so compare among tumor-only conditions).
We use CopywriteR - this uses off target regions to call copy number segments without need for a matched normal. Of course, you cannot differentiate between somatic and germline CNVs with just tumor samples.
You can use CNVKit to call CNV's from tumour only samples by creating a pooled reference from all the other bam files
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