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For the command line, create_ukbb_phenotype_dataset --phenotype-specs-file=./phenotype_specs.py --output-dataset-file=./ukbb_dataset.csv --output-covariates-columns-file=./ukbb_covariate_columns.json
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Hi, I just wonder what is the general speed for running ldpred2? I am running it for 2k samples with 512G mem which takes over one week. Is there a way to speed up the process? Thanks!
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I have installed PWAS. While it can't create a dataset and ran into the error.
[2022_11_02-10:03:46] Parsing the phenotype specifications...
Traceback (most recent call last):
File "/datalus/s…
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Hi,
Really scratching my head here with my mocha input. I have the phased annotated of my unphased file and I don't get any variants written to the allelic shift *as.bcf output. It worked in the …
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There seems to be UI error in showing biobank level sumstats for variants....
In either meta browser, go to any variant and sort by finngen pval or beta. Those with NaN there are completely in wrong…
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I was using regenie v3.2.5.2 with pgen input and the output contains an INFO column described in the documentation:
"**_With BGEN/PGEN files with dosages, the imputation INFO score is provided (IM…
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Hi there,
I have a dataset with 37k WGS, after doing my QC and using a MAF of 0.01 I am left with around 8M variants that I would like to use for running regenie.
I'm a bit confused on how to run …
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Hi there,
I am having trouble getting a global docker image working via my extras.json:
```
{
"defaultRuntimeAttributes" : {
"docker" : "dx://ukbb_wgs_test1:/docker_images…
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Hi Davide,
could you please fix the PRS script to include dosages for all UKBB individuals in the PRS calculation?
Thank you!
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Hi to everyone,
I want to use Regenie to test the association between rare variants and a pheno of interest. Currently I am using UKBB data.
To perform the step 1 I have run the following command:
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