Comments (1)
szhan
commented on July 28, 2024
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.
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Related Issues (12)
- Replace use of `tsinfer.SampleData` with `sgkit` HOT 3
- Use Dask to distribute runs of `tskit.lshmm` HOT 1
- Split `prepare_dataset.ipynb` into separate notebooks HOT 4
- Test sensitivity of sample matching to exact values of mismatch probabilities and switch probabilities HOT 1
- Choice of genotype array to generate pseudo-chip data
- Investigate differences in imputation results between `tskit.lshmm` and BEAGLE HOT 2
- Convert `run_lshmm.ipynb` into pipeline
- Call `bgzip` and `bcftools` from Python
- Check switch site positions in HMM copying paths HOT 2
- Looking into the source code of BEAGLE HOT 6
- Compare sample paths obtained using `_tskit.lshmm` and Duncan's 'lshmm'
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