commands

python filter.py --tcga-root /home/databank/gxxu/TCGA/ --manifest /home/databank/gxxu/tool/Manifest/ > filter/20240714.txt

python validate.py ../PAAD/Source/Norm/ -o validate/validate_paad_norm.csv > ./validate/paad.txt

python match.py -d /home/databank/gxxu/TCGA/CHOL/Source/Tumor -o ./match/chol_tumor_ma.csv -s /home/databank/gxxu/TCGA/Samplesheet/gdc_sample_sheet.Tumor_chol.tsv

 nohup python mutation_preprocess.py --input ../../CHOL/Source/Tumor/WXS_Somatic/ --output ../../CHOL/Source/Tumor/WXS_Somatic_processed > mut/chol_tumor_mut.txt 2>&1 &

 python methylation_preprocess.py -i ../../CHOL/Source/Tumor/Methylation/Sesame_Betas/ -o ../../CHOL/Source/Tumor/Methylation/Sesame_Betas_processed

  python cnv_preprocess.py --input_dir ../../ESCA/Source/Tumor/ASCAT_CNV/ --output_dir ../../ESCA/Source/Tumor/ASCAT_CNV_processed > ./cnv/esca_tumor_cnv.txt

 nohup Rscript cnv_preprocess.r  ../../CHOL/Source/Tumor/ASCAT_CNV/ ../../CHOL/Source/Tumor/ASCAT_CNV_processed >./cnv/chol_tumor_cnv.txt 2>&1 &

 nohup Rscript mutation_preprocess.r ../../CHOL/Source/Tumor/WXS_Somatic/ ../../CHOL/Source/Tumor/WXS_Somatic_processed >./mut/chol_tumor_mut.txt 2>&1 &

  nohup Rscript methyl_preprocess.r ../../CHOL/Source/Tumor/Methylation/Sesame_Betas/  ../../CHOL/Source/Tumor/Methylation/Sesame_Betas_processed >./methyl/chol_tumor_meth.txt 2>&1 &