How can I call somatic CNV in tumor samples with no normal samples?

Question

[Saurabh]

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?

Answer 1

[ultraanfibio]

Take a look at sarek: https://nf-co.re/sarek/3.4.0 I believe it supports tumor-only CNV calling

Answer 2

[QX]

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).

Answer 3

[Ram]

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.

Answer 4

[francisco]

You can use CNVKit to call CNV's from tumour only samples by creating a pooled reference from all the other bam files