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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…
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We run the gwas based on our WGS dataset ,so no imputation ,no INFO value. So is there no need to run the Quality Control of GWAS summary statistics?
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Thanks you for this greate tool to access GWAS catalog datasets. I want to download the top associations SNPs from GWAS catalog, and convert it to a SNP variant list like bim file,
![image](https…
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Dear professor,
We conducted an analysis using MTAG. Overall, the correlation between the effect sizes from MTAG and the original GWAS is quite good, r=0.67; however, we found that the effect sizes o…
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I'm getting the error Error in count.temp[, 2] : subscript out of bounds
while doing GWAS with InDel data. The updates don't seem to be helping. How should the input hapmap data look like to not g…
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Hi, I am comparing two big GWAS from the same paper. They are both big meta-analysis with the same sample, but from two different traits. For both sets of SNPs I have 27.000.000 SNPs so I run out of m…
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Please note - details below are going to be discussed in person next week.
See [here](https://genetics.opentargets.org/study/GCST002222) for current Open Targets Genetics study page.
- [ ] Scenari…
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This is my command:
!python /Users/halk/MetaXcan/software/SPrediXcan.py \ --model_db_path /Users/halk/Downloads/eqtl/mashr/mashr_Whole_Blood.db \ --covariance /Users/halk/Downloads/eqtl/mashr/mas…
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Hi @paul-shannon!
Last year, I pointed you out an issue about a color bug for GWAS tracks in igvR (the whole story [here](https://github.com/paul-shannon/igvR/issues/24)). It is still there in igv…
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Dear Dr. Zhou and colleagues:
**Can we use GEMMA to run a GWAS on UK Biobank data**?
I understand that I shall run each chromosome separately.
But still, if GEMMA only takes plink bed/bim/fam…