Markus Riester

Hi @sleyn I'm pretty sure this code pre-dates off-target support and also the switch from average coverage to counts. This code basically ignores the min.coverage when normalDB is provided because...

Oh. That explains some of the recent reports I got. I'll add the MBQ filter to PureCN.R. 20 is really low, but I see their concerns about PCR errors and...

What I'll do is to skip the filtering based on MBQ when too many variants are filtered out. Then the user can either lower the cutoff or do the filtering...

I decided to just throw a warning for now. The linked commit adds --min-base-quality to PureCN.R which you can set to 20.

Hi @jberg1999 , unfortunately the joint segmentation of multiple samples is currently not available because the copynumber package was removed from Bioconductor. But will get back to this soon, GATK...

That's a good starting point - if you are lucky and have multiple balanced segments with differing log ratio, it's usually pretty clear what is correct. With a bit of...

Ran into the same error. Installed a different package with mamba, which updated a long list of R related packages. After that it worked.

@zombiebride226 , pretty sure I'm not the best person to give advice, but in my case it was an old conda environment that didn't play nice with newer packages anymore....