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