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