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===Generating tped and tfam and methylation matrix files=== *TFAM awk '{print $2}' geno_GA.txt | sort -u > geno_GA.tfam (removed unwanted lines first) awk '{print sum" "$2" 0 0 0 -9"; sum++}' geno_GA.tfam > tmp vim tmp # add in number 30 for the first row. sort -k1,1n tmp > geno_GA.tfam *getChrPos.pl for rs sites ./getChrPos.pl geno_GA.txt < ../HsRef/Hg19/snp134_snv.txt > annotated.geno_GA.txt & *getTPED_11172011.pl ./getTPED_11172011.pl geno_GA.tfam < annotated.geno_GA.txt > geno_GA.tped & *Modified allBED2Matrix to get methylation matrix: The script was modified to read only 30 specified samples nohup ./allBED2Matrix.pl AMD-BED 27 1 0.1 > geno_GA_30.methylMatrix_min27_std0.1 & *Split CpGs file and run mQTL: split -l 10000 geno_GA_30* geno_methylMatrix_frag head -1 geno_GA_30* > header for f in geno_methylMatrix_frag* do cat header $f > tmp ./createPhenoFile.pl geno_GA.tfam tmp > $f done; mkdir phenoAB mkdir phenoAC mkdir phenoAD mkdir phenoAE mkdir phenoAF mkdir phenoAG mkdir phenoAH mkdir phenoAI mkdir phenoAJ mkdir phenoAK mkdir phenoAL mkdir phenoAM mv geno_methylMatrix_fragaa phenoAA/matrix.txt mv geno_methylMatrix_fragab phenoAB/matrix.txt mv geno_methylMatrix_fragac phenoAC/matrix.txt mv geno_methylMatrix_fragad phenoAD/matrix.txt mv geno_methylMatrix_fragae phenoAE/matrix.txt mv geno_methylMatrix_fragaf phenoAF/matrix.txt mv geno_methylMatrix_fragag phenoAG/matrix.txt mv geno_methylMatrix_fragah phenoAH/matrix.txt mv geno_methylMatrix_fragai phenoAI/matrix.txt mv geno_methylMatrix_fragaj phenoAJ/matrix.txt mv geno_methylMatrix_fragak phenoAK/matrix.txt mv geno_methylMatrix_fragal phenoAL/matrix.txt mv geno_methylMatrix_fragam phenoAM/matrix.txt for f in phenoA* do cd $f /media/2TB_store2/Dinh_Scratch/scripts/mQTL_2MB_plink.pl ../geno_GA matrix.txt > results.txt & cd .. done; *'''I still need to process the result files''' *Since this analysis was done on all GA (disease status samples), it might not be worthwhile to continue looking at this.
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