Methodology CNV subcommand

[Jens P.]

Hi,

is my assumption correct that the cnv subcommand is part of Delly since mid 2020?

I am interested to what extent the underlying methodology of this cnv subcommand differs from Delly as described in the paper from 2012 [1]?

Apart from the source code [2] and the README file [3], is there any further information or explanation on the methodology of the cnv subcommand?

Best regards,
Jens

[1] https://doi.org/10.1093/bioinformatics/bts378

[2] https://github.com/dellytools/delly/blob/main/src/cnv.h

[3] https://github.com/dellytools/delly/blob/main/README.md

[Tobias Rausch]

Hi Jens,

The 2012 paper only covers structural variant detection using short reads. It does not include genotyping, population calling, somatic workflows, long-read SV calling, and CNV methods. It's probably time for an updated manuscript, but I haven't managed yet time-wise. Briefly, the CNV calling uses mappability and GC fragment correction, and then segments the normalized copy number values. I'm afraid the only more detailed documentation is actually the source code.

Best, Tobias

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