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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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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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- 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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- 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.…
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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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This benchmark can be included in the TargetedEstimation.jl repo:
- [x] Define a UKBB-like task
- [x] Define a set of typical estimation strategies
- [x] Proceed to the run
- [x] Output the figures i…
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Hi,
I am getting following error while running finemapping. What might be the problem?
`cat sumstats.txt`
```
CHR SNP BP A1 A2 SNPVAR Z N
1 rs186077422 …
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- make optional for non-UKBB cohorts