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add work log gbm realign
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‎work_log_run_alchemist_b11

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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 1
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 2
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 3
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 4
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 5
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 6
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 7
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 8
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 9
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 10
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 11
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 12
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 13
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.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/cancer_gene_list_cell_uniq.tsv --step 14

‎work_log_run_confirmatory_gbm_realign.b2

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## b2 batch ##
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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#perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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
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perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.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

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