Rerun pipeline to match gnomAD release counts - HGDP

broadinstitute / gnomad_local_ancestry

Hail batch pipeline and scripts for local ancestry inference

MIT License

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Rerun pipeline to match gnomAD release counts - HGDP #110

Closed mike-w-wilson closed 3 years ago

mike-w-wilson commented 3 years ago

We did not filter to adj genotypes and allowed Eagle to impute genotypes. The pipeline needs to be rerun to filter to adj and then disallow imputation in eagle.

mike-w-wilson commented 3 years ago

Decided to just filter to adj genotypes during the vCF generation step as well -- filter out imputed and adj after tractor. This does not require a full rerun and should be relatively quick to do.