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Hi! I cannot see the definition of Effect column in the output file. And when I calculate, it is not the Odds Ratio based from the beta. What is the meaning of the Effect column and how was it comp…
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Hello, I would like to share an experience and a mistake I made during running the first step of REGENIE.
I ran REGENIE with the following code:
```
regenie \
--step 1 \
--bed BioVU_array…
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Hi,
I have a question about REGENIE v1.0.5.3. Can Step 1 run by splitting chromosomes such as inputting each chr bed file and output the .loco file for each chromosome?
Thanks a lot!
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Hi, I'm running Regenie Step2 on UK biobank RAP using swiss army knife.
This is my code:
length=23
start=1
for (( j=${start}; j
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I have 20K samples, and 150K variants. If we don't have limits on memory and number threads, what are the suggested flags to use to improve the speed. I am running below, it is taking too long (2hours…
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Hi Joelle, any chance of a release with everything included? The latest still giving trouble.
I can try and find an image but the last I found was v3.4
./regenie_v3.6.gz_x86_64_ubuntu20_mkl
./re…
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Hi @joellembatchou I'm trying to run regenie using the RAP system for UKB data. I have a WDL workflow created for this and was working fine while using bgen files as input. However I'm getting this er…
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Hi, We ran the gene burden test with the following command and found that some variants that were included in all the input files got excluded from the built mask (the .snplist output) or the final .R…
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Dear REGENIE developers,
I'm using REGENIE v3.5.gz on 237 cases and 387 controls. Genotypes of my samples were jointly called from WGS data, which had 50,811,891 variants. It was mentioned that 44…
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Hi all,
I would like to add bioconda containers for r-saige and regenie. I am not so sure how the relation between biocontainers and bioconda works. Do I have to make Dockerfiles and pull requests …