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When I use the following command:
_aldy profile --cn-neutral-region chr22:17400001-21700000 my.bam > my.profile_
I get the profile and when I use it in:
_aldy genotype -p my.profile -g cyp2d6 my.ba…
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When using pbstarphase for data analysis, I encounter an error: "assertion failed: phase_set.is_none()". However, if I exclude the genes CYP2C19 and VKORC1, the analysis works fine. Can you please hel…
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### Is there an existing module for this?
- [X] I have searched for the existing module
### Is there an open PR for this?
- [X] I have searched for existing PRs
### Is there an open issue …
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This is a sub-task of #2299.
- [x] Downweight text mining provider (need to discuss with @dkoslicki to find an appropriate example, so need to be postponed)
- [x] Downweight semmeddb
- [x] Single dru…
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Hello Steven, I am wondering if it would be possible to add the allelic depths to the data.tsv output in the results.zip.
This would be useful in knowing what the read-depth at the specific positio…
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As part of the Variant Page effort, we have discussed to start developing the first two widgets (sample data has been shared on slack):
- [x] ClinVar
```
{
"alleleOrigins": [
"germli…
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Hello,
PharmCAT/preprocessor: v2.9.0
Python: 3.9.13
JDK: jdk-17.0.4.1+1
Environment: Linux
Bcftools/bgzip/htslib: v1.18
Sorry for always coming with issues. I am working on setting up a pipe…
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**Is your feature request related to a problem? Please describe.**
The following CYP2D6 *6 haplotype is not called out by StellarPGx, for example:
"Sample core variants:
42128815~C>T~0/1;421290…
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Hello,
We have a number of short read whole genome sequencing samples (~200) where Aldy is unable to assign a genotype due to low coverage. I was able to successfully run Cyrius and PyPGx on most of …
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![image](https://github.com/sbslee/pypgx/assets/9035751/6fbabd8a-e144-4b3f-a2f0-3ddaace9c81b)
I have more than 100 samples.
When I use the VCFs (generated by Dragen/Illumina) as input it gives sim…