there are no Y chromosome variants

[JD12138]

Hi,
I am using your minicac graph.I noticed that there are no variants on chromosome Y in the vcf file that ready for panGenie(https://zenodo.org/record/6797328/files/cactus_filtered_ids.vcf.gz). I am confused. Could you tell me the reason?

[glennhickey]

attn: @eblerjana

[eblerjana]

This comes from an issue with filtering out variants from the MC VCF that are covered by less than 80% of the haplotypes. The current filtering pipeline does not handle cases with fully haploid chromosomes correctly. As a result, chrY is filtered out. Also, PanGenie's genotyping model is currently only designed for diploid chromosomes and might not handle fully haploid chromosomes (like chrY) correctly.