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Dear researchers,
Thank you for developing such an amazing tool. We recently conducted PRS-CS among UK Biobank (original genotypes without imputation), among 400,000+ SNPs, only 140,000 left for anal…
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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 guys,
I was reading the notebook for analyzing the UKB data [here](https://github.com/mcveanlab/treeseq-inference/blob/master/human-data/UKB_plot.ipynb). I was wondering if the output data at va…
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Hi,
Thank you for putting together such a great tool for researchers. I have a hopefully easy question, where does your list of hapmap variants come from? I've noticed some discrepancies between this…
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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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Dear SuSiE team,
I am a huge fan of your method and currently working on a pipeline to use SuSiE, susie_rss specifially, to finemap GWAS regions from UKBB data on binary traits. Although this seems…
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This is an attempt to collect all the Genetics Variant To Disease Pipeline steps to have an overall description of how it works and to identify points to work on to improve the overall functioning of …
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Hi Joelle,
In the documentation, it has been suggested that users should turn to pgen/bed files for analysing sex chromosomes:
> To include X chromosome genotypes in step 1 and/or step 2, males …
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Hi,
I may be quite wrong, but I was wondering why `set_snpid_index` in `parse` function behaves in a way that flips A1/A2 in the resulting dataframe index for some variants? I have a summary stat f…