-
Due to the small sample size of my target population, I was unable to isolate the validation population. I found the 'auto' and 'meta' version of the PRS-CSx algorithm can be used to construct a PRS, …
-
Hi,
First of all, I want to commend you on creating an impressive tool—great work! I have a few comments and questions that I hope can help clarify some aspects:
1. MAF vs. EAF in GWAS Datasets…
-
Task is to perform the harmonisation on GWAS Catalog summary statistics synched from the EBI FTP.
The full size of the dataset (on 2024-10-14) was:
```
❯ gsutil ls 'gs://gwas_catalog_inputs/raw_summa…
-
Hi MESuSiE developers,
Thank you for developing such a powerful tool for fine-mapping across multiple ancestries. I have two related questions that I hope you could help me with:
Handling Multip…
-
The function to generate the Manhattan plot requires the annotation column from the unitigs dataset (data/gwas/tet/tet_unitig_annotated_WHO_N.txt) (column position 9). However, the dataset only has 8 …
-
Hi there!
Thank you for the practical package. I have a question regarding the coloc.abf function when running it between my eQTL and GWAS data, both derived from the same samples. Here’s the code …
-
Hi, Zhili.
I am currently running SBayeRC for the first time on a phenotype of Anorexia Nervosa. The GWAS dataset I am utilizing is from 2019, which I have used in other approaches. However, I have e…
-
Hi when I run run_coloc.py:
python summary-gwas-imputation/src/run_coloc.py -keep_intermediate_folder -gwas_mode bse -gwas test1.txt -eqtl_mode bse -eqtl test2.txt -gwas_sample_size 149461 -eqtl_…
-
Currently the GWAS Catalog datasets are updated via [a shell script under /utils](https://github.com/opentargets/gentropy/blob/dev/utils/update_GWAS_Catalog_data.sh). However this is not the preferred…
-
We need to find a good dataset for testing the implementation of the pipeline.
This issue stems from a discussion documented here https://github.com/nf-core/gwas/issues/16#issuecomment-1030649162