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work_log_run_confirmatory_gbm_realign.b1
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work_log_run_confirmatory_gbm_realign.b1
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## b1 batch ##
#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 1
#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 2
#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 3
#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 4
perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 5
perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 6
perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 7
perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 8
perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 9
perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 10
perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 11
perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 12
perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 13