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Populate: Gene name, Callset freq, ClinVar significance
Remove: proband relationship, ancestry
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### Description of the bug
I have run PGSC_calc many times on different files but this is the only time I am running with liftover and with run_ancestry. Without run_ancestry, it runs fine. Otherwi…
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Hello,
I am currently using your Somalier software to check for relatedness and uniformly calculate ancestry PCAs across several cohorts for a meta-analysis. Our cohorts are mostly individuals with…
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With:
```python
import stdpopsim
sp = stdpopsim.get_species("StrAga")
contig = sp.get_contig(length=100000)
engine = stdpopsim.get_engine("msprime")
model = stdpopsim.PiecewiseConstantSize(sp.po…
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this is a feature suggest:
would it be possible to highlight the ancestry tree associated to given formula occurrence?
(e.g., on mouse-over on formulas)
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Hello,
I would appreciate your help with a question about ancestry composition.
Peddy assigns a single ancestry to each individual and gives the corresponding probability (which is the highest) …
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When searching by an Ancestry feat, the Reincarnated Feats should be disabled by default or at least being added to the Traits list and the Fey Influence feats should have a "pseudo trait" so we can d…
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Some places where additional cores may get a speed increase:
- [n_jobs](https://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestClassifier.html) in random forest classifier htt…
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input_datasets will be deprecated, and replaced with input_cohorts.
Ancestry plots relies on this param existing
https://github.com/populationgenomics/production-pipelines/blob/0ee315ef5de6c390c…
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There's a new format for the `ancestry` column which is more performant. Also, there's guidance on indexing that we'll want to make sure we follow. This column is used a lot so should make a noticeabl…