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I have been getting the same warning message when I tried to run LD clumping in plink and I have also tested different p1, p2 values.
here is my terminal output:
16384 MB RAM detected; reserving…
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Lirical 2.0.1 generates an extraneous tab in the column header for TSV outputs. This header specifies nine columns, but subsequent rows are only eight columns. Loading the TSV file into Python and s…
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Thank you to the PCN Toolkit team for this wonderful normative modeling resource.
I am getting unexpected metric results from my HBR model using pcntoolkit==0.29. I am adapting my code from the HBR…
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I have successfully run Step 1 computing the GRM on the fly. However, when I try using a sparse GRM computed through SAIGE (Step 0), the code initially runs but then gets stuck on the line "use sparse…
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I am getting the error below for step 1 regenie.
I have used this script for other datasets and had no issues.
How can i resolve thhis issue?
Options in effect:
--force-step1 \
--step 1 \…
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Hi, first of all thank you for this fantastic tool. I fully appreciate your hard work on maintaining regenie.
I have one question regarding the interaction test implemented in regenie. I am using v3.…
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For example, if I run step2 with 10 phenotypes the statistics are slightly different than if I run step2 with 2 phenotypes with all other inputs the same. The numbers are different enough that `np.isc…
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Hi!
I recently downloaded GWAS summary statistics for almost all UKBB phenotypes (both sexes only) via the AWS link found in the provided Google document. To ensure data integrity, I conducted an M…
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Hi!
Thank you for making this great tool available to the genetics field!
I am currently working with the UKB data and am performing an analysis using various combinations of masks and AF to tes…
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I went down a rabbit hole and want to pin this idea in case someone wants to take it up later: optimal fuzzy matches between the gsheet and CCV databases (or potentially any other database formats we …