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For some locations we seem to have LD showing alright, e.g. by HLA, while in other areas we aren't getting it for mostly (but will if we change to some other SNPs as the lead LD SNP, e.g. around TMEM1…
ttbek updated
3 years ago
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I'm writing a chapter on ``datalad push`` and was trying to outline how to do "common" workflows. It occurred to me that one standard workflow I use Git for is not possible solely with DataLad:
Pus…
adswa updated
3 years ago
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We are getting poor MNI normalizations (see images below) using fMRIPrep versions 20.1.1 and 20.2.0 LTS. We had good normalizations with version 20.0.6. I have not tested any other versions.
#…
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Hello,
can you advice on the best way to perform rare variants (MAF < 1%) analysis in Regenie?
Can this be supported via SPA / Frith correction?
So far I have tried the following:
```
pli…
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Hi,
I encountered following dividing zero error when running DENTIST on my data.
`[gz222@p02r09n24 10K]$ DENTIST --gwas-summary sim_1_cojo.txt --bfile /ysm-gpfs/pi/zhao/gz222/UKB_simulate/genot…
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For bgen data, we need a function that can produce hard calls from probabilities. This is necessary for calculating HWE in the UKB QC workflow (https://github.com/pystatgen/sgkit/issues/67). The fun…
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I'm getting some strange results with my own UK biobank + Biobank Japan data (the tutorial worked fine), where there are variants with extremely low p-values. I'm not sure what's causing this - most o…
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Hi Sam, I have a subgroup C from the UK biobank that I want to calculate PRSs for. If I only give phenotype file for C group versus for the entire cohort I get different PRS's. Do you know why this ma…
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The bug documented here occurs only in GKE and only when the files snakemake is downloading are sufficiently large: https://github.com/related-sciences/ukb-gwas-pipeline-nealelab/issues/20#issuecommen…
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construct an ontology for study_inHouseData