| MutSigPreprocess1 individual_set_id | GBM |
| MutSigPreprocess1 maf1 | MutSigPreprocess1.maf1.input.tsv |
| MutSigPreprocess1 maflabel1 | Broad |
| MutSigPreprocess1 maflabel2 | WashU |
| MutSigPreprocess1 maflabel3 | Baylor |
| MutSigPreprocess1 wig1 | MutSigPreprocess1.wig1.input.tsv |
| MutSigPreprocess1 build | hg18 |
| MutSigPreprocess1 context65_dir | /xchip/cga1/lawrence/db/context65 |
| MutSigPreprocess1 build_dir | /xchip/cga1/annotation/db/ucsc/hg18 |
| MutSigPreprocess1 num_categories | 4 |
| MutSigPreprocess1 target_list | /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt |
| MutSigPreprocess1 paramfile | /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt |
| MutSigRun3 individual_set_id | GBM |
| MutSigRun3 gene_list | /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt |
| MutSigRun3 build | hg18 |
| MutSigRun3 geneset_file | /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt |
| MutSigRun3 cosmic_file | /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv |
| MutSigRun3 refseq_file | /xchip/cga1/annotation/db/ucsc/hg18/R.mat |
| MutSigRun3 build_dir | /xchip/cga1/annotation/db/ucsc/hg18 |
| MutSigRun3 param_file | /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt |
| MutSigRun3 jobcount | 200 |
| CoMut4 individualSetId | GBM |
| GDAC_MutSig_Report6 ind_set | GBM |
| Execution Times: | |
| Submitted: | 15:32:57 30-08-12 |
| Completed: | |
| Elapsed: | 11 hrs 44 mins 05 secs |
step 1. MutSigPreprocess [id: 160748] preprocess patient list and mutations
urn:lsid:broadinstitute.org:cancer.genome.analysis:00272:90
| individual_set_id | GBM |
| maf1 | MutSigPreprocess1.maf1.input.tsv |
| maf2 | |
| maf3 | |
| maf4 | |
| maflabel1 | Broad |
| maflabel2 | WashU |
| maflabel3 | Baylor |
| maflabel4 | |
| wig1 | MutSigPreprocess1.wig1.input.tsv |
| wig2 | |
| wig3 | |
| wig4 | |
| build | hg18 |
| context65_dir | /xchip/cga1/lawrence/db/context65 |
| build_dir | /xchip/cga1/annotation/db/ucsc/hg18 |
| num_categories | 4 |
| target_list | /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt |
| paramfile | /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt |
| Output Files: | |
| GBM.mutation_preprocessing_report.txt | |
| GBM.coverage.prepare.txt | |
| GBM.maf | |
| GBM.patients.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 15:32:58 30-08-12 |
| Completed: | 15:35:50 30-08-12 |
| Elapsed: | 00 hrs 02 mins 52 secs |
step 2. ProcessCoverageForMutSig [id: 160749] processes coverage from wiggle files and does automatic category discovery
urn:lsid:broadinstitute.org:cancer.genome.analysis:00188:77
| coverage_prepare_file | GBM.coverage.prepare.txt |
| patient_list | GBM.patients.txt |
| mutation_list | GBM.maf |
| Execution Times: | |
| Submitted: | 15:32:58 30-08-12 |
| Completed: | 15:50:18 30-08-12 |
| Elapsed: | 00 hrs 17 mins 19 secs |
step 3. MutSigRun [id: 160750] perform MutSig calculations, generates output tables and report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:160
| individual_set_id | GBM |
| mutation_file | GBM.maf |
| coverage_file | GBM.coverage.mat |
| patient_file | GBM.patients.txt |
| category_file | GBM.mutcategs.txt |
| gene_list | /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010.genelist.txt |
| build | hg18 |
| geneset_file | /xchip/cga1/annotation/db/genesets/gsea_canonical_pathway_plus_HMT67.txt |
| cosmic_file | /xchip/cga1/annotation/db/cosmic/CosmicMutantExport_v48_260710_p25.tsv |
| refseq_file | /xchip/cga1/annotation/db/ucsc/hg18/R.mat |
| build_dir | /xchip/cga1/annotation/db/ucsc/hg18 |
| param_file | /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt |
| mutation_preprocessing_report_file | GBM.mutation_preprocessing_report.txt |
| jobcount | 200 |
| Execution Times: | |
| Submitted: | 15:32:58 30-08-12 |
| Completed: | 02:49:34 31-08-12 |
| Elapsed: | 11 hrs 16 mins 36 secs |
step 4. CoMut [id: 160751]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00488:7
| individualSetId | GBM |
| patientCRFile | GBM.patients.counts_and_rates.txt |
| mafFile | GBM.final_analysis_set.maf |
| mutcategsFile | GBM.mutcategs.txt |
| sigGenesFile | GBM.sig_genes.txt |
| Output Files: | |
| GBM_coMut.pdf | |
| GBM_coMut.png | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 15:32:58 30-08-12 |
| Completed: | 02:50:18 31-08-12 |
| Elapsed: | 11 hrs 17 mins 20 secs |
step 5. GenerateStickFigures [id: 160752]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00497:4
| maf | GBM.final_analysis_set.maf |
| sig_genes | GBM.sig_genes.txt |
| Execution Times: | |
| Submitted: | 15:32:58 30-08-12 |
| Completed: | 03:16:33 31-08-12 |
| Elapsed: | 11 hrs 43 mins 35 secs |
step 6. GDAC_MutSig_Report [id: 160753] Somatic Mutation Report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00413:16
| bar_plot | GBM.bargraphs.png |
| breakdown_table | GBM.mutation_breakdown.txt |
| categories_table | GBM.mutation_rates.txt |
| coverage png | GBM.covplot.png |
| sig_table | GBM.sig_genes.txt |
| cosmic_table | GBM.cosmic_sig_genes.txt |
| cosmic_table2 | GBM.cosmic_sig_genes2.txt |
| cosmic_muts_table | GBM.cosmic_mutations.txt |
| cluster_table | GBM.clustered_muts.txt |
| geneset_table | GBM.sig_genesets.txt |
| genset_table2 | GBM.sig_genesets_2.txt |
| patients_c_and_r | GBM.patients.counts_and_rates.txt |
| ind_set | GBM |
| mutsig_version | GBM.MutSig_version.txt |
| coMut_plot_png | GBM_coMut.png |
| coMut_plot_pdf | GBM_coMut.pdf |
| stick_figures_path | generatedStickFigurePaths.txt |
| maf_path | GBM.final_analysis_set.maf |
| mut_pre_rep_path | GBM.mutation_preprocessing_report.txt |
| mut_filt_rep_path | GBM.mutation_filtering_report.txt |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 15:32:58 30-08-12 |
| Completed: | 03:17:01 31-08-12 |
| Elapsed: | 11 hrs 44 mins 03 secs |
