ivargr

This might be because of something wrong i KAGE, so good that you reported. I think maybe there could be some roundoff error when writing genotype likelihoods so some become...

Would you be able somehow to share the kage index you are using and the reads you are using? That would make it a lot easier for me to debug...

I'm happy with anything, but the files may be too big for email? If email works in any way, you can email to [email protected].

Thanks for sharing! Is this when genotyping SVs or SNPs? Is this using any of the data you shared with me earlier?

Thanks for reaching out! I think the error is because KAGE needs a file as input for the reads. So using `

KAGE only works with GLIMPSE 1. I think as long as you have the GLIMPSE binaries in your path, that should work if the download fails. But I could add...

It is a bit difficult to know exactly why all genotype are 0/0 without looking at the data you used. However, I think your approach with only using 2 haplotypes...

Hi! Thanks for sharing! I'm a bit unsure what causes this problem. Does your VCF contain genotypes? Would you be able to share a small subset of the VCF, e.g...

Thanks for providing the vcf! I think the genotype columns in your vcf are invalid: ``` PN1 5147 >4637497>4637500 A T 60 . AC=2;AF=0.1;AN=20;AT=>4637497>4637499>4637500,>4637497>4637498>4637500;NS=20;LV=0 GT 0 . 0 0 ....

Ah, I see. So do I understand you correctly that the individuals are actually diploid, but they are purebred so that the genotype is always homozygous, so that `0` is...