Markus Riester

Thanks Ted for adding this to the tracker. This might take a while though.

Sure, feel free to send the main PDF + log. Happy to have a quick look.

Thanks Erik, will take care of this soon!

Hi, they are arbitrary and I’m open to improving them, i.e. open to suggestions. In some cases like Her2 you could optimize based on FISH concordance. In others that are...

Here some things I look first: https://github.com/lima1/PureCN/issues/230#issuecomment-1079140850 with a bit of experience, looking at the BAF plot quickly shows you if it looks good.

Really depends what you need. We sequence thousands of samples each year and don't go through them. Some cancer types such as lung are more difficult than others due to...

This is fairly old code and uses the first and last SNP on a chromosome to approximate start and stop. I'll change this soon, thanks for reporting.

Actually, now I remember why this is implemented that way. For LOH, SNPs define the resolution, so first and last SNP provide the area where we can call LOH. So...

Thanks, haven't seen this before. Which files does it generate (so I can figure out where it crashes)?

Hmm, never seen this before. Any chance you can share the Sampleid.rds and Sampleid.log files by mail with me?