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@hyanwong and I sat down and tried to think through properly how ancestral allele handling from sgkit should work.
The sgkit `variant_ancestral_allele` string array needs to be converted to a numer…
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In the ancestral allele inference, we filter the variants for SNPs, but we do allow multi-allelic SNPs since that is not a problem for the ancestral inference (it's just an allele count). However, som…
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E.g. using the new SGKit pipeline (files from http://hgdownload.cse.ucsc.edu/gbdb/hg19/1000Genomes/phase3/). I think we should allow reading of these files by default.
```python
from sgkit.io.vcf …
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Thorough testing will simplify development in the long run. It will help us to pick up mistakes sooner and make sure the pipeline runs on various datasets not only our personal favourites.
I think …
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Currently, the ancestral pipeline runs on the whole vcf at once. I think we should add a modification to be able to run by chromosome if needed for large datasets.
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As described briefly in https://github.com/tskit-dev/tsinfer/issues/228#issuecomment-734315735, it should be possible to use triallieic and tetraallelic sites for inference, rather than (as at present…
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It appears as if it's not possible to save an SgkitSampleData instance to a path. I'm not sure, therefore, how I might run the CLI on an zarr file, if I've specified bespoke masks, ancestral alleles, …
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```python
from pgmpy.models import BayesianModel
from pgmpy.estimators import BayesianEstimator
#model = BayesianModel([('Age', 'Pri'), ('Sex', 'Pri'),('Pri','Survived'),('Fare','Pclass'),('Pcla…
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Hi, thanks for this excellent piece of work! I am submitting what I think is a bug report, though it is possibly me not understanding the intended output of `augur ancestral`
**Current Behavior / S…
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See the note `SEMICOLON HERE RESULTS IN VentureRecords` in the code below:
```
new_traces = mapv(
proc(i) {
if (conditional && eq(i, CON…