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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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Hi there!
I have about 9700 genomic VCFs that I want to firstly filter using a BED file that defines about 500K SNPs, and merge into a single multisample VCF but as far as I can see, `gvcfgenotyper…
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Hi Florian,
Sorry for another question.
I am using ldpred2 to calculate polygenic risk scores. I am running the automatic model with the provided LD reference based on the example-with-provided…
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Hi Florian,
I am using LDpred2 to calculate polygenic risk scores. I am running the automatic model with the provided LD reference based on the example-with-provided-ldref.R.
I have three datas…
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https://github.com/andreyshabalin/simPRS
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Hi,
I'm running regenie on the UKBB data using the latest Docker Image and prepared the genotypes as described in the tutorial. This is the failed assertion I'm currently seeing:
```
block [594] …
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Hi,
I was wondering how I could view the sample IIDs within each specific quantile? I know the quantile.txt output shows you the number of samples within each quantile but can I view which samples …
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i tried to get PRSs according to various p-value thresholds, but i got exact same PRSs at different p-value settings.
here are my 3 different commands, which results same PRS.best
./PRSice_linu…
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Hi Bjarni,
Thank you for updating ldpred. I am having some trouble with step 2. I have successfully coordinated the data and am now trying to generated LDpred SNP weights. Regardless of the LDradiu…
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Hi, there:
I got a few theoretical and technical questions, listed below. It would be great if you guys could shed some light.
1. Figure 1 of the paper Sekar’s 2018 paper https://www.nature.c…