rgcgithub / regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.

https://rgcgithub.github.io/regenie

rgcgithub/regenie Issues

SNP has low variance.
Updated 24 days ago7
Quantitative phenotype processing - scaling, rint, and residualisation.
Updated a month ago2
Masks with unknown annotations do not work
Updated a month ago2
Strange Meta-Analysis Behaviour
Updated 2 months ago1
cannot write log file
Updated 2 months ago1
Document output format with `--htp` flag for region-based regenie step 2
Updated 2 months ago5
Add option to skip running the singleton mask
Updated 2 months ago
Using regenie for PheWAS with phenotypes with different missingness patterns
Updated 2 months ago
how the proportion of trait variance explained by causal SNPs is defigned
Updated 2 months ago
SKAT problems
Updated 2 months ago2
Second low variance error after filtering --mac 100 with Plink
Updated 3 months ago
incorrectly formatted phenotype file.
Closed 3 months ago1
Regenie ignores processing genes, but does not show any error
Closed 3 months ago3
not enough variants
Closed 3 months ago2
Number of ignored tests due to low MAC == 0
Closed 3 months ago4
Question about prediction in Step 1
Closed 3 months ago1
Consideration of multi-collinearity in covariates
Closed 3 months ago1
incorrectly formatted phenotype file.
Closed 3 months ago
the p value for ADD-INT_SNP is unresonable
Closed 3 months ago4
interaction test model
Updated 3 months ago
Step1 Firth fails to converge when running several phenotypes together
Updated 3 months ago2
segmentation fault using LD computation
Updated 3 months ago7
Annotation information could not be read
Closed 3 months ago1
Genotyped data for step 1>1M variants
Closed 3 months ago2
Question about using phenotype files for different populations in two steps
Closed 3 months ago1
covariance of interaction and snp terms
Closed 3 months ago3
Fraction of genes have no gene_p results
Updated 3 months ago3
Does Regenie implement internal variant filtering for building mask in rare variant burden testing?
Closed 4 months ago
ERROR: vector::_M_default_append
Closed 4 months ago2
genebase
Updated 5 months ago4
Feature request: E-value statistics
Updated 5 months ago1
Normalisation and scaling of the phenotypes
Updated 5 months ago2
Interaction test to output ADD-INT_SNPxVAR result
Closed 5 months ago7
Testing for interaction in gene-based test
Closed 5 months ago4
Burden testing issue - input variants not in snplist or masks_report?
Updated 5 months ago2
Is it possible to compute LD between two masks?
Closed 6 months ago5
All individuals have missing/invalid values for all traits
Closed 5 months ago3
empty output file
Updated 5 months ago1
DF column in the burden test
Updated 5 months ago1
Can the annotation file contain more than one annotation for same variant?
Closed 5 months ago1
Trying to download gz.sif file
Closed 6 months ago
feature request: select a range of phenotypes
Closed 6 months ago2
Robust SE when conducting interaction studies: the impact of phenotype scaling? --force-robust undocumented?
Closed 6 months ago1
Hail Implementation of Regenie Burden Testing
Closed 6 months ago1
Feature request: dominance deviation testing and improved recessive+dominance tests
Updated 6 months ago1
Does REGENIE step 1 require independent SNPs?
Closed 6 months ago2
--ref-first for pgen pvar psam files
Closed 6 months ago1
How REGENIE deal with missing genotype data while calculating LOCO score
Closed 6 months ago1
How to deal with INFO score for chromosome X?
Closed 6 months ago4
regenie step 1 :ERROR
Closed 7 months ago