Test using Shapeit4 with --use-PS option

broadinstitute / lrma-aou1-panel-creation

Pipelines and evaluations covering integration, phasing, and imputation of short and structural variants for the AoU Phase 1 long-reads callset.

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Test using Shapeit4 with --use-PS option #14

Closed rlorigro closed 1 month ago

rlorigro commented 1 month ago

As @hangsuUNC identified, Shapeit4 has an option to respect phase blocks, we should see if it helps with incompatible haplotype generation

rlorigro commented 1 month ago

Very curious about the results from this. Does --use-PS affect the incompatible alleles?

samuelklee commented 1 month ago

See the comments in the PR, it appears to have a positive effect. Although it might be nice to see this vary as a function of the argument and perhaps also over a larger region.