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  1. Working on the Research Analysis Platform
  2. Running analysis jobs

SAIGE

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

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Last updated 1 year ago

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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