weizhouUMICH SAIGE issues

weizhouUMICH / SAIGE

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Not equal number of samples in sample and bgen file

#397 Alireza-Majd closed 2 years ago
1
Error in step2 of saige gene for some genes in group file

#396 aokulabasile closed 2 years ago
1
Updates to variant_group_iterator

#395 jonathonl closed 2 years ago
0
pcg did not converge

#394 ytao0210 closed 2 years ago
2
Abnormal output of SAIGE step 2 with "idstoIncludeFile" parameter

#393 XiangyuYe closed 2 years ago
4
pcg did not converge in step1

#392 shimaomao26 closed 2 years ago
6
Large sample size analysis requires more time

#391 ytao0210 closed 2 years ago
0
Download failed with error 503 for: //tukaani.org/xz/xz-5.2.3.tar.bz2

#390 lanxianmei closed 2 years ago
1
"isSparse" not found

#389 oalavijeh closed 2 years ago
3
Coding sequencing batch as a covariate

#388 tylim closed 2 years ago
1
Burden test produced lower P value than SKAT-O

#387 aoxiang88 closed 2 years ago
1
Single marker analysis for all the variants including MAC<3 in the whole exome sequencing data

#386 iamhere218 closed 2 years ago
2
Error at Step2 of gene-based analysis: getDosage_bgen_withquery_Sparse() : BGenError

#385 JingxuanBao closed 2 years ago
1
Error Step 2: The number of samples specified in the sample file does not equal to the number of samples in the bgen file

#384 Mahmedturk closed 2 years ago
2
Error at step2 running gene-based testing: has N = 0 (mismatch with header block)

#383 xmduumich closed 2 years ago
1
Memory issue in step2_SPAtests.R in version 0.44 but not in 0.42

#382 adrlar closed 2 years ago
1
Limit BLAS thread usage in Step2, fixing a repeatedly reported problem with resource usage.

#381 pettyalex closed 2 years ago
0
High thread usage and long run time in step2_SPAtests.R

#380 pettyalex closed 2 years ago
2
Is it possible to perform only genotype Quality Control with SAIGE?

#379 raimondsre closed 2 years ago
2
SAIGE single variant error for allocate large memory

#378 ypnngaa-py closed 2 years ago
1
Error in obj.null$XV %*% G

#377 liwangchang closed 2 years ago
1
Same values in pvalue and pvalue.na fields

#376 aritra90 closed 2 years ago
1
Memory Issue for SAIGE-GENE step 0 (create sparse GRM) using UKBB WES data

#375 ypnngaa-py closed 2 years ago
2
SAIGE combined pathway enrichment analysis?

#374 Shicheng-Guo closed 2 years ago
1
Same script but different results

#373 Abdelrahman-Galal closed 2 years ago
1
Can SAIGE handle NAs in phenotype file

#372 adanordeidet closed 2 years ago
1
SAIGE-0.44.6.1 step2_SPAtests.R Error

#371 liwangchang closed 2 years ago
1
step2_SPAtests.R ignores --vcfFileIndex in v0.44.6.5

#370 nkgx closed 2 years ago
5
Memory error during step2_SPATests.R

#369 Xophmeister closed 2 years ago
2
Open VCF failed

#368 lgb-cyber closed 2 years ago
4
Error: variants must be biallelic

#367 sarahcolbert closed 2 years ago
1
Not sure if LOCO=TRUE worked

#366 adanordeidet closed 2 years ago
1
SAIGE-based principal components GWAS

#365 rbutleriii opened 2 years ago
0
Error in SAIGE on bioconda

#364 Amelia-uoft closed 2 years ago
2
Unexpected behavior of SAIGE-GENE+ in step 2 (a possible bug?)

#363 Ojami closed 2 years ago
4
Problem installing savvy

#362 Reavyr closed 2 years ago
1
RHS 'b' has wrong number of rows: gene based tests

#361 complexgenome closed 2 years ago
3
SAIGE step2 error

#360 lanjblue closed 2 years ago
3
SAIGE-GENE+ document update?

#359 Ojami closed 2 years ago
0
SAIGE memory error

#358 lanjblue closed 2 years ago
1
https://pheweb.org/MGI-BioVU/about

#357 Shicheng-Guo closed 2 years ago
1
Error in gzfile(file, "wb") : cannot open the connection

#356 SYSUMSD closed 3 years ago
1
Install error-Failed to build package statgen/savvy

#355 ZD-Mei closed 2 years ago
2
Error with numeric headers in step 1

#354 yningvu closed 2 years ago
1
leave-one-chromosome-out can't be conducted

#353 r-mustafa closed 2 years ago
1
Can I run SAIGE for every chromosome separately?

#352 hehongyi closed 2 years ago
1
step1_fitNULLGLMM: plink files from TOPMED imputation || Error for bad alloc

#351 complexgenome closed 2 years ago
5
Error running burden tests on autosomes + chrX at the same time

#350 Alexander-Stuckey closed 2 years ago
1
fillNULLGLLM error

#349 rtooze closed 2 years ago
1
Running step1 only for variance ratio

#348 ErikAUT closed 3 years ago
0

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