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astheeggeggs / lshmm

code to run Li and Stephens
MIT License
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Change query input to API #133

Closed szhan closed 1 week ago

szhan commented 1 week ago

In the diploid case, the input data should be a reference panel of phased haplotypes and a query of unphased genotypes (encoded as allele dosages). Currently, the API functions take queries of phased haplotypes.

szhan commented 1 week ago

I also tweaked the simulation parameters to get ref. panels and queries that meet certain criteria (e.g. enough sites but not too many).