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CTLife · Sep 20, 2022 · 8dbab91 · 8dbab91
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diff --git a/10a_cis_permutation.1.sh b/10a_cis_permutation.1.sh
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+#####################
+file1=merged
+inputPath=4a_keptPeaks
+
+out=10a_cis_permutation.optimize.peaks
+mkdir  $out
+
+
+out1=$out/1.0
+mkdir -p $out1
+QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz         \
+             --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+
+
+out1=$out/onlyKnown
+mkdir -p $out1
+QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz      --cov  PCA_PEER/BA9.knownFactors.all.txt   \
+             --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+
+
+for n in $(seq 1 3); do
+    out1=$out/1.$n
+    mkdir -p $out1
+    QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz    --cov  7a_Peaks_Factors/PCA/PCA.$n.txt    \
+                 --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+done  
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diff --git a/10a_cis_permutation.2.sh b/10a_cis_permutation.2.sh
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+
+#####################
+file1=merged
+inputPath=4a_keptPeaks
+
+out=10a_cis_permutation.optimize.peaks
+
+for n in $(seq 4 8); do
+    out1=$out/1.$n
+    mkdir -p $out1
+    QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz    --cov  7a_Peaks_Factors/PCA/PCA.$n.txt    \
+                 --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+done  
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diff --git a/10a_cis_permutation.3.sh b/10a_cis_permutation.3.sh
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+
+#####################
+file1=merged
+inputPath=4a_keptPeaks
+
+out=10a_cis_permutation.optimize.peaks
+
+
+for n in $(seq 9 12); do
+    out1=$out/1.$n
+    mkdir -p $out1
+    QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz    --cov  7a_Peaks_Factors/PCA/PCA.$n.txt    \
+                 --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+done  
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diff --git a/10a_cis_permutation.4.sh b/10a_cis_permutation.4.sh
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+
+#####################
+file1=merged
+inputPath=4a_keptPeaks
+
+out=10a_cis_permutation.optimize.peaks
+
+
+for n in $(seq 13 16); do
+    out1=$out/1.$n
+    mkdir -p $out1
+    QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz    --cov  7a_Peaks_Factors/PCA/PCA.$n.txt    \
+                 --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+done  
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diff --git a/10a_cis_permutation.5.sh b/10a_cis_permutation.5.sh
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+
+#####################
+file1=merged
+inputPath=4a_keptPeaks
+
+out=10a_cis_permutation.optimize.peaks
+
+for n in $(seq 17 20); do
+    out1=$out/1.$n
+    mkdir -p $out1
+    QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz    --cov  7a_Peaks_Factors/PCA/PCA.$n.txt    \
+                 --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+done  
+
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diff --git a/10b_cis_permutation.1.sh b/10b_cis_permutation.1.sh
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+
+#####################
+file1=merged
+inputPath=4b_keptGenes
+
+out=10b_cis_permutation.optimize.genes
+mkdir  $out
+
+
+out1=$out/1.0
+mkdir -p $out1
+QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz         \
+             --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+
+
+out1=$out/onlyKnown
+mkdir -p $out1
+QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz      --cov  PCA_PEER/BA9.knownFactors.all.txt   \
+             --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+
+
+for n in $(seq 1 3); do
+    out1=$out/1.$n
+    mkdir -p $out1
+    QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz    --cov  7a_Peaks_Factors/PCA/PCA.$n.txt    \
+                 --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+done  
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diff --git a/10b_cis_permutation.2.sh b/10b_cis_permutation.2.sh
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+
+#####################
+file1=merged
+inputPath=4b_keptGenes
+
+out=10b_cis_permutation.optimize.genes
+
+for n in $(seq 4 8); do
+    out1=$out/1.$n
+    mkdir -p $out1
+    QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz    --cov  7a_Peaks_Factors/PCA/PCA.$n.txt    \
+                 --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+done  
+
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diff --git a/10b_cis_permutation.3.sh b/10b_cis_permutation.3.sh
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+
+#####################
+file1=merged
+inputPath=4b_keptGenes
+
+out=10b_cis_permutation.optimize.genes
+
+for n in $(seq 9 12); do
+    out1=$out/1.$n
+    mkdir -p $out1
+    QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz    --cov  7a_Peaks_Factors/PCA/PCA.$n.txt    \
+                 --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+done  
+
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diff --git a/10b_cis_permutation.4.sh b/10b_cis_permutation.4.sh
@@ -0,0 +1,26 @@
+
+#####################
+file1=merged
+inputPath=4b_keptGenes
+
+out=10b_cis_permutation.optimize.genes
+
+for n in $(seq 13 16); do
+    out1=$out/1.$n
+    mkdir -p $out1
+    QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz    --cov  7a_Peaks_Factors/PCA/PCA.$n.txt    \
+                 --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+done  
+
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diff --git a/10b_cis_permutation.5.sh b/10b_cis_permutation.5.sh
@@ -0,0 +1,26 @@
+
+#####################
+file1=merged
+inputPath=4b_keptGenes
+
+out=10b_cis_permutation.optimize.genes
+
+for n in $(seq 17 20); do
+    out1=$out/1.$n
+    mkdir -p $out1
+    QTLtools cis --vcf   0_BAM/Phenotype_Genotype/BA9_samples.MAF15.vcf.gz       --bed  $inputPath/$file1.sorted.bed.gz    --cov  7a_Peaks_Factors/PCA/PCA.$n.txt    \
+                 --permute 1000    --std-err  --out $out1/$file1.permutation.txt  --log $out1/$file1.Log   >  $out1/$file1.runLog.txt 2>&1
+done  
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