Kez Cleal

Thanks! Supplementary mappings are really handy for calling SVs, so would be great if you can implement this

Hi, thanks for pointing this out, python 3.10 is not yet supported on pypi. I will add this to the documentation. Im not sure why you needed to install numpy...

Thanks for raising this. Could you try `pip install dysgu==1.3.4`? Im not sure what is causing this yet, but looking in to it. Would you be able to post the...

The latest version on pypi is only 1.3.5 https://pypi.org/search/?q=dysgu. I'm wondering if this is a problem with xcode? See this post: https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a

It is confusing. I have not problems building with clang, so not sure what is going. The other option would be to try docker. I will get try and get...

Hi @Taalouane I think your approach seem reasonable. Only one thing that I can suggest - where you re-genotype at the sample level, you should probably explicitly remove the target...

Hi @johannesgeibel, I think I understand what you mean. The original workflow aims to try and avoid double counting the original variant, as you say. The input sites shouldn't influence...

I think this sounds reasonable. Additionally, I apologize, but I found a bug when I was reviewing the code - I realized the option `--parse-probs` was always being treated as...

Hi, There currently is no model for PacBio CLR, although I plan to add one. For now, using nanopore model would probably work best. I will leave this open until...

Thanks for raising this, it looks like `--recursive` does not fetch htslib properly. You can download from the release though instead e.g. `wget https://github.com/kcleal/dysgu/releases/tag/v1.3.12`