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Also encountered "The estimated prior variance is unreasonably large" using ieugwasr ld_matrix_local function to calculate the ld matrix. As I have checked the original code of _ld_matrix_local_ func…
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Hi,
I found a huge discrepancy in the genetic correlation & mean of chi^2 between LDSC and MTAG.
LDSC = 0.47 vs. MTAG = 0.27
Do you have any idea? Please help.
LDSC:
Heritability of phenoty…
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Here is an updated example of a BCF file on bluecrystal4:
```
/mnt/storage/private/mrcieu/research/mr-eve/gwas-files/2/data.bcf
```
Ultimately we would like to have a report for all `gwas-file…
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When I call ./ldsc_preprocess.py -h it runs and I successfully get the "sg.txt.gz" and "ce.txt.gz". However when I attempt to check the log file I get the following error:
ValueError: Found Allele …
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Dear CheckSumStats workgroup member
Sorry for taking your time.
It has been a while that I got the following error for using "make_plot_gwas_catalog" function. I tried several times with different t…
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## 1. Bug description
Hi I am unable to properly run finemap_loci with a quantitative GWAS.
Few things to highlight so far.
- The sample size column to do finemapping for a quant GWAS is not …
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Dear Team,
I am calculating Partition heritability , but I am getting error of "parsing annotation error". Can you please help me with this? Here is my command:
GWAS trait: PASS.Bipolar_Disorder_AL…
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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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Hi,
I want to run smilenfer for some quantitative traits. I have been able to reproduce the test trait (bc), but am wondering what I should change in the analysis pipeline to run quantitative trait…
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## 1. Bug description
Any parquet functions cause a segfault error when running unit tests with "Test" or "Check" buttons in Rstudio, but not when running manually or with "Run test" button.
###…