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eblerjana / pangenie

Pangenome-based genome inference
MIT License
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Which version of CHM13 reference genome to use #31

Closed Han-Cao closed 1 year ago

Han-Cao commented 1 year ago

Hi,

Thanks for developing this great tool. I would like to use the "HPRC-CHM13 (88 haplotypes)" variant reference. Based on the name, I think the reference genome I should use for genotyping is CHM13, but I am not sure which version of CHM13 to use. Could you provide links to the reference genome you used when generating the variant reference vcf?

Thanks, Han

eblerjana commented 1 year ago

Hi Han,

I'm using this reference: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph/CHM13v11Y.fa.gz

Best, Jana

Han-Cao commented 1 year ago

Hi Jana,

Thanks a lot! This is really helpful.

Best, Han