somatic copy number calling with ONT long-reads

Question

[eebloom]

Looking for suggestions of a somatic CNV caller suitable for nanopore long-reads (tumour). I have already tried CNVkit but would be ideal to generate a consensus from multiple callers.

Answer 1

[GenoMax]

Spectre and QDNAseq are included in nanopore's human variation pipeline: https://github.com/epi2me-labs/wf-human-variation

[eebloom]

I was recently told that these are not very suitable for somatic /cancer data so was looking for tools more tailored to tumour sequencing.

I do see that spectre has a --cancer parameter but Im not sure exactly how effective this is / what it does