A tool to perform genome-wide association tests in large-scale data sets and biobanks


For general tips on troubleshooting, see guide.

IssueExample error messageWhat to do

Issue with input

Value provided for input field "" could not be parsed as file: could not resolve "" to a name or ID

Check that the input file path you specified is correct

Error fitting null model (Step 1)

cannot stat '/home/dnanexus/*.sparseSigma.mtx: No such file or directory

In SAIGE GWAS GRM app, set Is Sparse K In = True. This parameter can be found in the SAIGE-GENE section

SPAGMMAT test error (Step 2)

Error in SPAGMMATtest(vcfFile = opt$vcfFile, vcfFileIndex = opt$vcfFileIndex, :

467880 samples have been used to fit the glmm null model

chromosome 0 is out of the range of null model LOCO results

Specify "--chr" under the input "Extra Options".

See the following github issue.

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