How do you create the SparseSigmafile?

[Ruedog]

use --sparseSigmaFile to specify sparse Sigma file generated in step 1. Note: not sparse GRM

IsSingleVarinGroupTest=TRUE is to perform single-variant assoc tests as well for markers included in the gene-based tests

only vcf, sav, and bgen dosage file formats can be used for gene-based tests

to perform gene-based tests, --groupFile is used to specify a group file

Each line is for one gene/set of

variants. The first element is for gene/set name. The rest of

the line is for variant ids included in this gene/set. For

vcf/sav, the genetic marker ids are in the format

chr:pos_ref/alt. For begen, the genetic marker ids should

match the ids in the bgen file. Each element in the line is

seperated by tab.

Rscript step2_SPAtests.R \ --vcfFile=./input/seedNumLow_126001_seedNumHigh_127000_nfam_1000_nindep_0.sav \ --vcfFileIndex=./input/seedNumLow_126001_seedNumHigh_127000_nfam_1000_nindep_0.sav.s1r \ --vcfField=DS \ --chrom=chr1 \ --minMAF=0 \ --minMAC=0.5 \ --maxMAFforGroupTest=0.01 \ --sampleFile=./input/samplelist.txt \ --GMMATmodelFile=./output/example_binary.rda \ --varianceRatioFile=./output/example_binary_cate.varianceRatio.txt \ --SAIGEOutputFile=./output/example_binary_cate.SAIGE.gene.missingness.txt \ --numLinesOutput=1 \ --groupFile=./input/groupFile_geneBasedtest.txt \ --sparseSigmaFile=./output/example_binary_cate.varianceRatio.txt.sparseSigma.mtx \ --IsOutputAFinCaseCtrl=TRUE \ --IsSingleVarinGroupTest=TRUE