ivargr

Great! Let me know if you run into any other issues :)

Hi! Thanks for reaching out! There's been a lot of development on KAGE the last days and unfortunately not so good testing. I was able to reproduce your error, and...

It seems like this happens when the reference genome does not have the same chromosome order as the VCF. I've pushed a fix for this now (`pip install kage-genotyper==0.2.7` should...

Hi! That's an interesting question. I'm not familiar with genotyping using ancient DNA, but I think a challenge might be that KAGE relies on relatively good prior probabilities of genotypes...

Yes, this might be possible! Unfortunately, the indexing is a bit cumbersome and havn't been tested well on other species than human, but should in theory work. Do you have...

Sorry for taking some time to get back to you! This repository should now contain step-by-step instructions on how to build indexes from a reference and a set of variants:...

Hi! Thanks for asking! Yes, the index creation step does only support biallelic VCFs for now (since we want to represent each variant using two nodes in the graph), so...

If you want to share the VCF and reference genome you want to create indexes for, I'll be happy to try to create the indexes (will be useful for debugging/trying...

Hi! Sorry, there seems to have been a mismatch in the code after I've updated some indexes. I pushed a fix now, so it should be fixed in latest version...

Sorry for the late reply! This error message should have been clearer, but this is because you have Ns in your sequences. Am I correct that some of your reads...