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szhan / onekg_analysis

Evaluation of genotype imputation methods using the unified genealogy dataset
MIT License
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Initial analysis #6

Closed szhan closed 1 year ago

szhan commented 1 year ago

This shows the entire workflow mostly in Jupyter notebooks.

szhan commented 1 year ago

The wrongly imputed genotypes using tskit.lshmm are far too high to make sense. In contrast, the imputed genotypes from BEAGLE almost perfectly agree with truth. I suspect that the step adding new sample edges to the reference tree seqsuence is not done correctly. So, next thing is to investigate that step.