Create AMR reference panel for RFMix

broadinstitute / gnomad_local_ancestry

Hail batch pipeline and scripts for local ancestry inference

MIT License

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Create AMR reference panel for RFMix #29

Closed mike-w-wilson closed 3 years ago

mike-w-wilson commented 3 years ago

pops for Native American component: 1kg: PEL

HGDP: Colombian Karitiana Maya Pima Surui

mike-w-wilson commented 3 years ago

Meeting with Marcos Santoro and Elizabeth on July 16th to discuss his findings on optimal reference panel composition.

mike-w-wilson commented 3 years ago

Marcos suggested the sample samples as above for the Native American component of the reference panel -- he recommended using the PEL samples that cluster closest to the other HGDP samples and drop the others. His work also showed that two and three way admixed samples can use the same reference panel.

mike-w-wilson commented 3 years ago

Final reference is 241 samples: gs://gnomad-mwilson/lai/sample_selection/ref_to_run.tsv