Compare results of tskit.lshmm and BEAGLE using correct BEAGLE VCF file

szhan / onekg_analysis

Evaluation of genotype imputation methods using the unified genealogy dataset

MIT License

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Compare results of tskit.lshmm and BEAGLE using correct BEAGLE VCF file #26

Closed szhan closed 1 year ago

szhan commented 1 year ago

I used the wrong target VCF file for input to BEAGLE (full set), so that's why the imputed genotypes were in nearly perfect agreement with the true genotypes. The majorly corrected results now make sense, in line with previously obtained results using FinnGen data.