New sequenza version

[Sequenza User Group]

Dear all,

After loosing the copynumber package dependency (it was removed from BioC since unmaintained) we were looking for alternative way to update the package to have it available on CRAN again.

Copynumber was a technically important dependency, since we were using its segmentation algorithm.

Luckily, we implemented our own segmentation algorithm now, and we will soon release an almost completely rewritten version of sequenza (4.0?).

Since it was a good opportunity to revisit the old rusty structure that I developed.. wow 10 years ago!.. for my PhD project, there will be new functionalities, such as subclonal quantification and workflow for panel sequencing, and probably also some changes in the command lines/arguments.

We also drastically changed the workflow. We suggest to use sequenza using results from germline and somatic variant calls, eg VCFs from strelka and mutect combines with a serie of sequenza-utils commands to generate a small seqz file (runtime ~5 minutes) that provides more or less the same information that the bigger files generated by parsing BAM file directly (runtime ~8-12h). Of course we will keep the parsing from BAM as an option.

We are still far away from release, since the code now need compilation in C++, but I would like to hear from people that uses sequenza other than me, what would you like to be fixed/added in a new release?

Thanks and enjoy the upcoming holiday period :)

Francesco