Determine official AMR LAI subset

broadinstitute / gnomad_local_ancestry

Hail batch pipeline and scripts for local ancestry inference

MIT License

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Determine official AMR LAI subset #90

Closed mike-w-wilson closed 3 years ago

mike-w-wilson commented 3 years ago

Ensure removal of v3.1:: samples and TGP dups if exist consider using Julias recently run relatedness check.

mike-w-wilson commented 3 years ago

AMR subset is 7612 samples: gs://gnomad-mwilson/lai/sample_selection/amr_to_run.tsv. This set contains all inferred AMR released samples that were not included in the reference panel. HGDP samples are not included as they make up the Continental American component of the reference panel. TGP was included as they are not in the reference.