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somatic copy number calling with ONT long-reads

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.

ont somatic cancer cnv nanopore
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written by eebloom • eebloom

1 answer

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

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written by GenoMax GenoMax

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

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written by eebloom • eebloom

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