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Hello,
I wonder how longphase handles supplementary alignments during phasing and haplotagging; as a separate read or they inherit HP/PS of the primary alignments.
Thank you,
Ayse
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### Description of the bug
Hello from Lund! Trying to get Tomte up and running. The stub run works fine, but running into some errors running on real data.
The error:
```
$ cat .command.err
U…
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Processing my input data with your preprocessing and annotation pipelines, I get the input files for running the seed gene discovery pipeline (except the phenotypes parquet, which I created).
In `rul…
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Hi,
I got a error when `test dynamic allelic imbalance`,
```
y
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Hello @zengxiaofei ,
I used hifiasm with hifi and HiC data, and generate haplotype-specific data, including p_ctg.fa, p_utg.fa, r_utg.fa, and hap*.p_ctg.fa.
As you mentioned in the tutorial, if I wa…
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Hi,
When I'm running this step in https://deeprvat.readthedocs.io/en/latest/annotations.html#running-the-pipeline:
```
(deeprvat_annotations) pichuan@pichuan-gpu:~/deeprvat/example/annotation…
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Hi there,
Thanks for creating this wonderful package.
I've read your recent biorxiv paper on HGSOC ("Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational proc…
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Hi,
I came across your package a couple days ago by searching and found your newly released vignettes. Since I'm working on a project involving calculation of allelic imbalance, thought why not to gi…
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Hi!
I encountered a similar issue as previously reported. During the initial attempt, ASCAT failed to determine an optimal ploidy. However, on a subsequent trial with extensive min_ploidy and max_p…
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**1. What were you trying to do?**
Use `vg call` to genotype a graph.
**2. What did you want to happen?**
Have heterozygous variants called as heterozygous.
**3. What actually happened…