Christoffer Flensburg

Hi! These exact filtering strategy, cuts and choices like these evovled over years, especially at the start of the development. Every choice is a compromise between sensitivity and accuracy and...

If you just want to check specific variants in a limit number of samples, then I'd just look them up in the allVariants.Rdata output after the superFreq run. That has...

Oh I had forgotten that there is a manual, thanks for that! :D I am not quite sure what you are referring to though. Shaved? Setting somaticP to 0.99 should...

Hi! Yep, our institute told me about a year ago that I was essentially the only user on their gitlab that had any regular external traffic, and that they wanted...

Thanks. So seems I left a lot of URLs still pointing to the WEHI gitlab. Guess it's still been online until a certificate expired between your last use. I'll update...

The resource directory is meant to be re-used like this, which is why the option is there. It's resources like the mm10 genome sequence, gene regions, COSMIC mutation frequencies and...

Ahh, yes I forgot the capture regions, sorry. The .bed file with the exons (the padded regions where it's looking for variants in an exome) is not in the resource...

I am still working on this. A bit slower than expected, but not forgotten.

Hi! Yep, there were some delays, but it's done and up live now. I found some half-done fixed for (unrelated) annotation issues that I wanted to fix before pushing live....

SuperFreq roughly goes as 1) sort variants into somatic, germline heterozygous, and other (noise, germline homozygous, ..) 2) use germline hets and read counts for CNA calling 3a) use the...