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qtl_cmd.sh
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qtl_cmd.sh
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#if there is no sample relatedness in the data set, GRM is not needed to fit the null model
##--useGRMtoFitNULL=FALSE
#if there is sample relatedness in the data set, use a sparse GRM
##--sparseGRMFile=nfam_5_nindep_0.mtx \
##--sparseGRMSampleIDFile=nfam_5_nindep_0.mtx.sampleID \
##--useSparseGRMtoFitNULL=TRUE \
#we always use a plink file that contains 2000 independent markers (LD pruned) to estimate a variance ratio
##--plinkFile=
Rscript step1_fitNULLGLMM_qtl.R \
--sparseGRMFile=./input/nfam_5_nindep_0.mtx \
--sparseGRMSampleIDFile=./input/nfam_5_nindep_0.mtx.sampleID \
--useSparseGRMtoFitNULL=TRUE \
--phenoFile=./input/seed_1_nfam_5_nindep_0_ncell_100_lambda_50_withCov_Poisson.txt \
--phenoCol=y \
--covarColList=PC1 \
--sampleIDColinphenoFile=IND_ID \
--traitType=count \
--outputPrefix=./output/poisson_test \
--skipVarianceRatioEstimation=FALSE \
--isCovariateOffset=FALSE \
--isCovariateTransform=FALSE \
--skipModelFitting=FALSE \
--plinkFile=./input/nfam_500_nindep_5000_step1-nodupSNPs \
--IsOverwriteVarianceRatioFile=TRUE &> ./output/poisson_test.log
Rscript step1_fitNULLGLMM_qtl.R \
--useGRMtoFitNULL=FALSE \
--phenoFile=./input/seed_1_nfam_5_nindep_0_ncell_100_lambda_50_withCov_Poisson.txt \
--phenoCol=y \
--covarColList=PC1 \
--sampleIDColinphenoFile=IND_ID \
--traitType=count \
--outputPrefix=./output/poisson_test \
--skipVarianceRatioEstimation=FALSE \
--isCovariateOffset=FALSE \
--isCovariateTransform=FALSE \
--skipModelFitting=FALSE \
--plinkFile=./input/nfam_500_nindep_5000_step1-nodupSNPs \
--IsOverwriteVarianceRatioFile=TRUE &> ./output/poisson_test.log
#Run a single variant association tests
Rscript step2_tests_qtl.R \
--bedFile=./input/nfam_500_nindep_5000_01.bed \
--bimFile=./input/nfam_500_nindep_5000_01.bim \
--famFile=./input/nfam_500_nindep_5000_01.fam \
--AlleleOrder=alt-first \
--SAIGEOutputFile=./output/nfam_500_nindep_5000_01_poisson_single \
--chrom=1 \
--minMAF=0 \
--minMAC=5 \
--LOCO=FALSE \
--GMMATmodelFile=./output/poisson_test.rda \
--varianceRatioFile=./output/poisson_test.varianceRatio.txt \
--is_noadjCov=TRUE \
--is_sparseGRM=FALSE \
--markers_per_chunk=10000 \
--pval_cutoff_for_fastTest=0.05 \
--SPAcutoff=10000 \
--is_EmpSPA=FALSE &> ./output/nfam_500_nindep_5000_01_poisson_single.log
#Run a group tests
Rscript step2_tests_qtl.R \
--bedFile=./input/nfam_500_nindep_5000_01.bed \
--bimFile=./input/nfam_500_nindep_5000_01.bim \
--famFile=./input/nfam_500_nindep_5000_01.fam \
--AlleleOrder=alt-first \
--SAIGEOutputFile=./output/nfam_500_nindep_5000_01_poisson_set \
--chrom=1 \
--minMAF=0 \
--minMAC=5 \
--LOCO=FALSE \
--GMMATmodelFile=./output/poisson_test.rda \
--varianceRatioFile=./output/poisson_test.varianceRatio.txt \
--is_noadjCov=TRUE \
--is_sparseGRM=FALSE \
--markers_per_chunk=10000 \
--pval_cutoff_for_fastTest=0.05 \
--SPAcutoff=10000 \
--is_EmpSPA=FALSE \
--annotation_in_groupTest=lof:missense \
--maxMAF_in_groupTest=0.5 \
--groupFile=./input/nfam_500_nindep_5000_01_group.txt &> ./output/nfam_500_nindep_5000_01_poisson_set.log