saigegit / SAIGE

Development for SAIGE and SAIGE-GENE(+)

saigegit/SAIGE Issues

v1.3.3 vs v1.3.6
Updated 3 months ago
Question about including chrX and Y
Updated 3 months ago
Discrepancy between reported P value and P value calculated from Z statistic
Updated 4 months ago
Step 1 with sparse GRM gets stuck on "use sparse kinship to fit the model"
Updated 4 months ago
ERROR: Reading nth marker failed.
Closed a year ago2
Question about burden inflation versus skat-o
Updated 5 months ago
specifying sparseGRM files in step 2 for single variant tests
Closed 5 months ago
Error: vector::_M_range_check: __n (which is 2538) >= this->size() (which is 2538)
Updated 6 months ago1
Question about `LOCO`
Updated 6 months ago
Error in SPAGMMATtest ... merge bmerge Incompatible join types: x.ID (integer) and i.SNP (character)
Updated 7 months ago1
Duplicate IDs in phenotype input crash step 2
Updated 8 months ago
Error: vector::_M_range_check: __n (which is 2538) >= this->size() (which is 2538)
Updated 8 months ago3
Q: length dosages in DS VCF field
Updated 8 months ago
SAIGE installation error
Updated 9 months ago1
memory allocation failure in step1
Updated 9 months ago4
Error running SAIGE using unimputed data
Updated 10 months ago1
Error during conditional analysis
Updated 10 months ago
Install problem
Updated 10 months ago
SAIGE not installing on R 4.3.2
Updated 10 months ago1
Getting this error while running saige on chromosome X
Updated a year ago1
SAIGE step 1 using the whole genome separate chromosome specific to
Updated a year ago3
Too high value of Varratio_NULL
Updated a year ago
Installation from the source code Step 3 Issue: leeshawn/MetaSKAT and Rcpp
Closed a year ago1
Discrepancy in number of variants used for set-based test and single association analyses.
Closed a year ago
SAIGE STEP2 does not accept plink files
Closed a year ago1
error: Error in getopt(spec = spec, opt = args) : long flag "bedFile" is invalid
Closed a year ago10
fitNULLGLMM spsolve(): memory allocation failure
Updated a year ago
fitNULLGLMM: glmmkin.ai_PCG_Rcpp_Binary -> Get_Coef -> getCoefficients - spsolve(): memory allocation failure
Closed a year ago4
SAIGE step 2 *** caught segfault *** address 0x448, cause 'memory not mapped'
Updated a year ago
Trying to get LOCO=True to work
Updated a year ago
Step1, sorting of sample ids
Updated a year ago
Use of SAIGE-GENE+ GLMM approach for predictive modelling
Updated a year ago
createSparseGRM script (step0) doesn’t work
Updated a year ago1
Parsing errors when covariate names include symbols (gram+, gram-)
Updated a year ago
Producing groupFiles from entire chromosome data
Updated a year ago1
Error(s) during WES analysis on UKBB
Closed a year ago1
Should I use imputed data for the plink file in step 1 of SAIGE instead of the diierct genotype data of the SNP array?
Updated a year ago
SNP POS should not use scientific expression
Updated a year ago
Running step2 in subsets of genomic regions
Updated a year ago
samples in geno file do not have phenotypes
Closed a year ago
ERROR! bed file does not exsit
Closed a year ago2
Saige gwas giving SE == 0
Updated a year ago3
Can you please create tags for released versions?
Updated a year ago2
Dominant and Recessive models
Updated a year ago
ERROR: 2 has Phased = 2 (not 0)
Closed a year ago1
floating point exception raised during step2 SPAtests
Updated a year ago1
Error while installing saige in slurm module
Closed a year ago1
Minor allele count in SAIGE vs SAIGE-GENE
Closed a year ago1
SAIGE License Clarification
Updated a year ago
Saige Docker in google cloud registry
Closed a year ago6