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Hi Sam,
I was trying to compute PRS from UKBB BGEN v1.2 files but ran into an error using PRSice v 2.3.5. Below are my commands and outputs.
```
Rscript ./PRSice.R --dir . \
> --prsice ./PRSic…
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Hi I am trying to apply PRScsx using my genotyping data, this is how my code looks like, please help me to solve this issue
python PRScsx/PRScsx.py --ref_dir=/hpf/projects/arnold/data/g…
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* In attempting to run the latest version (v0.2.2) on a UKBB subject I get an early failure during surface creation.
The call made:
```
apptainer run --cleanenv \
-B ${WORKDIR}/bids:/bids …
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Hi,
I was trying to follow the examples in R/Example, but was not able to download classic LTFH to source it. The webpage "https://alkesgroup.broadinstitute.org/UKBB/LTFH/" shows some error, and I …
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Hi!
I'm trying to run pong, but when specifying the ind2pop file I keep getting this error message:
"error: individual population file assignment contains more than 1 column of data"
However, m…
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Hi,
I read the new version of the tutorial on polygenic risk scores (https://privefl.github.io/bigsnpr/articles/LDpred2.html) as well as your preprint on LDpred2-auto (https://www.biorxiv.org/conte…
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This is an imputation on the UK Biobank data using minimac 1.0 on chr7. I am getting a similar error on other chromosomes. Any suggestions for this? This job is running with 28 cores and 196 GB of…
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- compatible with non-UKBB cohorts
- objectives:
1. change UKBB_BED_FILES and UKBB_BGEN_FILES to just BED_FILES and BGEN_FILES
2. add COHORT
3. QC_FILE, TRAITS_CONFIG and WITHDRAWAL_LIST optional
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Hi Joelle,
I was wondering why REGENIE relies on AAF instead of MAF in region-/gene-tests? MAF seems more intuitive compared to AAF (similar to what SAIGE-GENE does)? This can be problematic when A…
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- make compatible with non-UKBB cohorts
- objectives include:
1. QC file as an optional argument
2. update generateIIDGenotypes workflow (and consequently IIDGenotypes which contains filterBed)
3.…