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Multi-allelic vcf may cause error in building index

3

Hi, I've been trying to build my own index bundle to use with kage, but keep encountering errors along the way. I believe the most recent on is due to...

ASLeonard

kage installation error

2

I install kage via `pip3` which works fine: ``` pip3 install kage-genotyper ``` However, when I try to run it I get: ``` cgroza@ubuntu:~$ kage Traceback (most recent call last):...

cgroza

Haploid Haplotype Reconstruction

1

@sandve, I am working on reconstructing a haploid haplotype using the imputed genotypes from KAGE. Currently, I am using the following commands: ```bash kage index -r MHC-CHM13.ref.fa -v MHC_49-MC.vcf.gz -o...

gsc74

Error when running kage index

5

Hi, I'm trying to run the kage index step of kage but I get the following error: TypeError: __init__() missing 1 required positional argument: 'dtype' My input VCF is only...

zhiyaoma2t