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Hello,
I was trying to work on some UK biobank data and followed the instructions on the recommendations for UK Biobank analysis page. After I filtered the original bgen file using plink, 237514 snps…
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Dear developers of nadavbra/ukbb_parser,
after following through the installation and configuration as described on the Code page, and trying out the parser via Python, I get the error message: mod…
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conda install -c stracquadaniolab -c bioconda -c conda-forge baghera
doesn't seem to function.
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Hi,
I got this error:
```
File "/home/hao/Project/sopNMF_atlas/scripts/tasks/IWAS_ICD10/2_IWAS_analysis_UKBB_ICD.py", line 100, in lm_pvalue
results = model_all.fit(n_jobs=8)
File "/…
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I have been trying to use the snp_readBGEN() function on one of the genotype datasets in our lab for use with LDpred2. Currently though I have repeatedly been getting the error:
Error in { :
ta…
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are you planning to include the "polyfun version" of files related to --ref-ld-chr and --w-ld-chr in your download ftp site:
https://data.broadinstitute.org/alkesgroup/LDSCORE/
python polyfun.p…
bnj50 updated
2 years ago
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Hi Sam,
Apologies if I have missed how to do this on the ‘available commands’ page, but I would like to obtain results for pre-specified SNP inclusion thresholds (e.g., 0.01, 0.05, 0.1, 0.5, 1) rat…
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Hi @nadavbra,
thank you again for helping with my previous question. Working with the ukbb_parser, another two questions came up:
I would like to generate a table that looks like this in the end:
I…
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The preprocessing script (make_finemap_inputs.py) includes a flag to filter out the MHC region from possible credible set regions. However, it only filters out lead variants. If a lead variant is righ…
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currently using UKBB design.fsf; need to create one for Cam-CAN task data