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### Description of the bug
Hello!
Firstly, thank you for the tool.
I used it long time ago, and now tried to install the newest version (v2.0.0-beta.3) using
```
nextflow run pgscatalog/pgsc_calc…
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Hi Kai,
Hope all is well.
Could I ask if you have plans to provide support for plink2 in [SuSiEx_LD.py](https://github.com/getian107/SuSiEx/blob/master/utilities/SuSiEx_LD.py)? We have a large a…
cqgd updated
8 months ago
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whole genome association analysis toolset
https://www.cog-genomics.org/plink2
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### Description of the bug
Pipeline execution:
- Initial run: Failed, error reported missing .pgen file.
- Rerun with '-resume': Same error occurred.
1. Versions: Nextflow 24.04.4, Java 11.0.2…
Fiwx updated
2 months ago
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Thanks for developing this method. I've run into a potential bug where Ne estimates are different depending on the input file. I'm happy to share example files if that is helpful.
In short, given t…
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Hi developer,
Thanks for developing this nice package. I was wondering if we have the plan to support plink2 format in the future.
Thanks!
Yanyu
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https://explore.anvilproject.org/datasets/1cfec078-e268-44b8-b2ed-39aa8c45d939 and
https://explore.anvilproject.org/datasets/1cfec078-e268-44b8-b2ed-39aa8c45d939
Have markdown in them for example.
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I noticed that create_prs_metrics.R considers Plink1 format score files i.e. `.profile` files. However, Plink2.0 gives output as `.sscore` instead.
Could Plink2.0 support be also considered in [cre…
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Hello,
I am planning a large-scale neuroimaging analysis that would also require extracting individual univariate GWAS results for each phenotype. Would you be able to advise on how the computatio…
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Modules to be created as per individual steps in the original imputation pipelines
```yaml
# step-0
- awk
- check_vcf_build.R
# step-1
- plink
- plink2
- LiftMap.py
- chainfiles
- b…