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run_saige_subset_chr21_1pct.qsub
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run_saige_subset_chr21_1pct.qsub
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#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -q short.q
#$ -r yes
#$ -l mem_requested=50G
#$ -N run_saige
#$ -o stdout_run_saige_CD4_NC_sub_1
#$ -e stderr_run_saige_CD4_NC_sub_1
#$ -t 1-300
# #$ -m ae
# #$ -M a.cuomo@garvan.org.au
i=${SGE_TASK_ID};
chrom=21
gene_name=$(sed "${i}q;d" /directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/input/power_analysis_subsets/gene_lists/chrom21_genes.txt)
regionFile="/directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/input/power_analysis_subsets/cis_region_files/${gene_name}_cis_region_1Mb.txt"
R_PATH=/share/ScratchGeneral/anncuo/jupyter/conda_notebooks/envs/RSAIGE/bin/
cd /share/ScratchGeneral/anncuo/software/qtl/extdata
${R_PATH}/Rscript step1_fitNULLGLMM_qtl.R \
--useSparseGRMtoFitNULL=FALSE \
--useGRMtoFitNULL=FALSE \
--phenoFile=/share/ScratchGeneral/anncuo/OneK1K/saige_eqtl/input/Sept23/SCT/CD4_NC_sc_pheno_cov_1pct_subset.tsv \
--phenoCol=$gene_name \
--covarColList=age,sex,pc1,pc2,pc3,pc4,pc5,pc6,pf1,pf2 \
--sampleCovarColList=age,sex,pc1,pc2,pc3,pc4,pc5,pc6 \
--sampleIDColinphenoFile=individual \
--traitType=count \
--outputPrefix=/directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/output/subsets/subset_1pct/${gene_name}_1pct_CD4_NC_poisson_test \
--skipVarianceRatioEstimation=FALSE \
--isRemoveZerosinPheno=FALSE \
--isCovariateOffset=FALSE \
--isCovariateTransform=TRUE \
--skipModelFitting=FALSE \
--tol=0.00001 \
--plinkFile=/directflow/SCCGGroupShare/projects/anncuo/OneK1K/plink_files/plink_pruning/chr2_pruned_sc_samples \
--IsOverwriteVarianceRatioFile=TRUE &> /directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/output/subsets/subset_1pct/${gene_name}_1pct_CD4_NC_poisson_test_`date +%Y-%m-%d.%H:%M:%S`.log
${R_PATH}/Rscript step2_tests_qtl.R \
--vcfFile=/directflow/SCCGGroupShare/projects/anncuo/OneK1K/genotypes/filter_vcf_r08/chr${chrom}.dose.filtered.R2_0.8.vcf.gz \
--vcfFileIndex=/directflow/SCCGGroupShare/projects/anncuo/OneK1K/genotypes/filter_vcf_r08/chr${chrom}.dose.filtered.R2_0.8.vcf.gz.csi \
--SAIGEOutputFile=/directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/output/subsets/subset_1pct/${gene_name}_1pct_CD4_NC_poisson_test_cis \
--chrom=$chrom \
--minMAF=0 \
--minMAC=20 \
--LOCO=FALSE \
--GMMATmodelFile=/directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/output/subsets/subset_1pct/${gene_name}_1pct_CD4_NC_poisson_test.rda \
--SPAcutoff=2 \
--varianceRatioFile=/directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/output/subsets/subset_1pct/${gene_name}_1pct_CD4_NC_poisson_test.varianceRatio.txt \
--rangestoIncludeFile=${regionFile} \
--markers_per_chunk=10000 &> /directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/output/subsets/subset_1pct/${gene_name}_1pct_CD4_NC_poisson_test_cis_`date +%Y-%m-%d.%H:%M:%S`.log
# ${R_PATH}/Rscript step3_gene_pvalue_qtl.R \
# --assocFile=/directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/output/subsets/subset_1pct/${gene_name}_1pct_CD4_NC_poisson_test_cis \
# --geneName=$gene_name \
# --genePval_outputFile=/directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/output/subsets/subset_1pct/${gene_name}_1pct_CD4_NC_poisson_test_cis_genePval
qstat -j $JOB_ID > /directflow/SCCGGroupShare/projects/anncuo/OneK1K/saige_eqtl/output/subsets/subset_1pct/${gene_name}_1pct_CD4_NC_poisson_test_cis_`date +%Y-%m-%d.%H:%M:%S`_qstat.txt