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## Describe the issue
Hello, I'm testing v113 using the v113 docker obtained from docker hub and the v113 cache downloaded using the following command:
`docker run --network host -t -i -v /mnt/data1…
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**Describe the bug**
My goal is to have a list of different things in a JSON file. I rely on Pydantic to parse the content. I don't want to use `isinstance`, rather all these different things impleme…
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- [x] Write script that generates folder structure to run the access pipeline.
This should consist of the following:
1. Given a project, create the project folder if it exists skip it.
2. …
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We'll need something like this to segregate indels, MNPs or larger structural variants from snps in certain analyses, and it could start by simply defining an `is_snp` function. That would be enough …
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**Describe the bug**
VarDict SVs once again end up in the SNV VCF files, making them hard to visualise for the user when loaded in Scout.
**To Reproduce**
Load e.g. case `novelbear` (or presumabl…
dnil updated
7 months ago
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I understand that it has not been published, and I do not know if it has been benchmarked in any way. But in theory Pangenie offers variant phasing via an hmm-based algorithm, which seems sensible.
…
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Hi,
I split the 1000GP chrX VCF into nonPAR, PAR1, and PAR2 regions then tried creating .msav files with these but I encountered some issues. Below is the code I used.
```bash
#/usr/bin/env bas…
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Hi there,
I am trying to run the pipeline on some older fastq files (circa 2010s) using the docker profile. The reads for the files are relatively short at ~75bp. Following previous advice from Abh…
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Hello, we are running cases on trios and we're trying to find structural variants mainly in the child.
I am from a computer science background so I don't have full picture of how some of these parame…
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This is a new iteration of the data, making #3567 obsolete:
```
❯ gsutil ls gs://ot_orchestration/releases/24.10_freeze2/
gs://ot_orchestration/releases/24.10_freeze2/locus_to_gene_gold_standard.json…