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From https://opain.github.io/GenoPred/pipeline_technical.html#Workflow my understanding is that sumstat_prep step is done independnetly from format_target step, thus internal score files (produced by …
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make sure all the scheduled slurm jobs in scrontab have an error and output dir instead of using sportbot home dir by default.
among those jobs:
- [x] FTP SYNC (prod, dev)
/hps/software/users/parki…
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Hi , I am getting the following error. I was attempting to use a different GWAS sumstat with the test target data and it keeps getting stuck on this error.
Error in rule prep_pgs_lassosum_i:
…
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### Is your feature request related to a problem? Please describe.
I'm a new user and have downloaded the large volume of `vcf`-type files required to act as the reference.
### Describe the sol…
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Data associated with this project https://www.medrxiv.org/content/10.1101/2023.12.06.23299426v1 has been shared with Open Targets and needs ingesting into the GWAS Catalog. The data is presented in se…
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As a **community user** I want **to be able to understand how the Gentropy ariflow pipeline works ** because **I want to reproduce it with nextlfow.**
## Background
Background to this task is a res…
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Hi,
Thanks for the invaluable tools and tutorial resources you provided!
I am currently working with imputed data from the UK Biobank, and I have encountered a challenge regarding the storage si…
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### System information
_No response_
### Description of the Issue
Hello, I installed gwas-sumstats-tools in a conda environment. But I get the following error message when I run gwas_ssf.
(gwas-su…
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We encountered some troubles in the process of testing the GWAS-SVs pipeline with the GATK due to the lack of JSON files for module7. I wonder if you can share the JSON file in Module 7 (in developmen…
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Hi, I was trying a first run with GWAs summary statistics and encountered the below error. I was using the sparse LD matrix based on hapmap ukbEUR. I had downloaded the matrices available here: https:…