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I was just going through the tutorial I got the following "error messages"- is this something I should be worried about?
```
$ pypgx run-ngs-pipeline CYP2D6 grch37-CYP2D6-pipeline --variants "/hom…
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CYP2D6 kcat labelled as renal plasma clearance in the table in section 2.2.1
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Hi, thank's for the hard work in this pipeline.
Everything works fine with the test dataset, but it reported error with real pacbio `subread.bam` file.
Here is the command which I use.
```sh
➜ n…
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Hi, as discussed in #32, I want to integrate CNV/SV called by other tools with PyPGx pipeline. Most of the time, those CNV/SV are stored as VCF file, while PyPGx need the CNV/SV to be labelled as in `…
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**Describe the bug**
Run StellarPGx with docker implementation on CYP2C9 gene.
I have run StellarPGx for around 1000 samples with different genes (CYP2D6, CYP2C19, etc.) with no problem, but with CY…
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Hi, I am working with Aldy and need to provide --phase parameter for more accurate calling of novel star alleles.
I used HapCUT2, based on the related documentation and received both "haplotype_outpu…
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Hi, this question is mostly for better understanding of pypgx data structure.
I tried to figure out the meaning of RefAllele, but it's not quite right actually. I thought RefAllele is the allele re…
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Sorry for being so dumb, but I see a lot of documentation on how to create and save models, but not load them and use them for new predictions--is that documented somewhere?
For example, I have th…
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### Week 1 - Get to know the community
- [x] Join the communication channels
- [x] Open a GitHub issue (this one!)
- [x] Install the Ersilia Model Hub and test the simplest model
- [x] Write a motiva…
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get_depth step failing. It looks like the sample.recal.bam.bai file is not copied over to work_dir.
The run error:
```
[E::idx_find_and_load] Could not retrieve index file for 'sample.recal.bam…