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eblerjana / pangenie

Pangenome-based genome inference
MIT License
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Joint-genotyping across samples #18

Open jjfarrell opened 2 years ago

jjfarrell commented 2 years ago

Is there a way to generate a joint-genotyped vcf with pangenie? If I understand the software correctly, only the variants in the pangenome reference are called across all the genotyped samples while the non-pangenome variants detected are called within individual samples.

eblerjana commented 2 years ago

No, unfortunately there is no joint genotyping mode. PanGenie genotypes a single sample in each run. Also, PanGenie is a re-genotyping method, so it only genotypes the variants contained in the pangenome input VCF. It does not detect any new ones.