SAIGE

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

Troubleshooting

For general tips on troubleshooting, see guide.

Issue	Example error message	What 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.