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Hello,
I am trying to calculate a PRS-score, with PRSice2, on a case-control-cohort based on summary statistics from a larger GWAS-study. I have calculated principal components and want to use the fi…
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This is an estimate of the VM rental time necessary to do the GWAS regressions (similar to https://github.com/related-sciences/ukb-gwas-pipeline-nealelab/issues/8).
Here are current figures:
- T…
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Hi, I am new here.
when i tried to run my data I encounter this issue everytime.
ERROR converting summary statistics:
Traceback (most recent call last):
File "./munge_sumstats.py", line 61…
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Hello,
I want to use the numpy inspired API to open an bgen using a symbolic link. I want to do this because I don't want to create the .metadata2.mmm file in the shared directory where the bgen li…
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Hi,
I am running Predict.py with some bgen files. I actually have two issues. The first is that I am unable to pass sample IDs. I tried supplying the sample file with the --text_sample_ids command bu…
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https://cran.r-project.org/web/packages/MendelianRandomization/index.html
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We would like to have panUKBB LD matrixes to improve our finemapping process.
3 ancestries: EUR, AFR, CSA
s3://pan-ukb-us-east-1/ld_release/UKBB.EUR.ldadj.bm
s3://pan-ukb-us-east-1/ld_release/U…
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Our download access to https://biobank.ctsu.ox.ac.uk/ is ending on 2021-08-18.. We need to archive as much as possible to our internal servers before that date.
Their download docs are https://biob…
kousu updated
3 years ago
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After some discussion the bcf format is moving to a slightly modified vcf format (see https://github.com/MRCIEU/gwas_harmonisation/issues/15 for info)
I have made a new branch in this repository ca…
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Hi,
I'm trying to use CARMA to finemap. However, I run into an issue where I'm getting multiple variants fine-mapped to high PIPs despite these variants being in strong LD with each other.
As …