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What's the best way to spend my money on hardware, if I'd like to run SAIGE-GENE on a plink file with 2k samples and a WES data after QC, preferably using docker? How many cpu cores can be utilised in…
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Hi there, I'd like to ask if the use of snp_PRS() is compatible with BGEN file input? And if so, is the dosage data hard-coded?
Thanks
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### What you did:
We want to use the ancestry classification tool to predict genetic ancestry of UKBB samples. (https://gnomad.broadinstitute.org/news/2021-09-using-the-gnomad-ancestry-principal-co…
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Hi,
Thanks for updating REGENIE again - we've really appreciated the software you've made available in our department.
I've found that when running any SKAT/ACAT test, I get the following error:…
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Hello,
I am using UK biobank 500k imputed data for a gene-based analysis. for traits with sample size > 340k (quantitative traits) or 230k (binary traits) I get below error:
*** caught segfault *…
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## Background
We want to explore extracting gene/disease associations from the exome sequencing analyses carried out by Regeneron Genetics Center.
Their work is collected in their recent [publicat…
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The Interaction Learner: Interaction Transformer + Generalized Linear Model (Logistic regression mostly I think) seems to fail to converge on the UKBB data. this need investigation.
TODO:
- [x] …
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I have a quick question; I am working in African ancestry for both target dataset and summary statistics.
I noticed that in the ldpred2 paper, the European LD reference is available at https://doi.o…
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I installed using conda baghera-v2.1.11 and received the below error when running baghera on the ldscore_folder and GTF file (step1).
("baghera-tool -h" command work well)
NameError: name 'folder…
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Hi there!
I am running LDSR analysis using the package you developed, as well as LDSC. However, I noticed that the results (i.e., intercept and h2 estimate) from bigsnpr and LDSC are not similar ev…