This usecase describe how to run Bolt-LMM analysis (https://alkesgroup.broadinstitute.org/BOLT-LMM/BOLT-LMM_manual.html). All commands below assume that $COMORMENT, $SIF and $SINGULARITY_BIND environmental variables are defined as described in the INSTALL file.
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Create the required LD and pheno files to run Bolt-LMM from here
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Run the analysis for demo data using gwas.sif container
singularity exec --home $PWD:/home $SIF/gwas.sif bolt --bfile=/REF/examples/regenie/example_3chr --phenoFile=bolt_out/example_3chr.lmm.pheno --phenoCol=PHENO --verboseStats --LDscoresFile=bolt_out/example_3chr.LDSCORE.tab --covarFile=/REF/examples/regenie/covariates.txt --qCovarCol=V{1:3} --modelSnps=bolt_out/example_3chr.snplist --statsFile=bolt_out/example_3chr_bolt.stats