| MutSigPreprocess1 individual_set_id | LAML |
| MutSigPreprocess1 maf2 | MutSigPreprocess1.maf2.input.tsv |
| MutSigPreprocess1 maflabel1 | Broad |
| MutSigPreprocess1 maflabel2 | WashU |
| MutSigPreprocess1 maflabel3 | Baylor |
| MutSigPreprocess1 wig2 | MutSigPreprocess1.wig2.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 | LAML |
| 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 | LAML |
| GDAC_MutSig_Report6 ind_set | LAML |
| Execution Times: | |
| Submitted: | 16:24:46 16-08-12 |
| Completed: | |
| Elapsed: | 08 hrs 20 mins 11 secs |
step 1. MutSigPreprocess [id: 146765] preprocess patient list and mutations
urn:lsid:broadinstitute.org:cancer.genome.analysis:00272:90
| individual_set_id | LAML |
| maf1 | |
| maf2 | MutSigPreprocess1.maf2.input.tsv |
| maf3 | |
| maf4 | |
| maflabel1 | Broad |
| maflabel2 | WashU |
| maflabel3 | Baylor |
| maflabel4 | |
| wig1 | |
| wig2 | MutSigPreprocess1.wig2.input.tsv |
| 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: | |
| LAML.mutation_preprocessing_report.txt | |
| LAML.maf | |
| LAML.coverage.prepare.txt | |
| LAML.patients.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:24:46 16-08-12 |
| Completed: | 16:31:58 16-08-12 |
| Elapsed: | 00 hrs 07 mins 12 secs |
step 2. ProcessCoverageForMutSig [id: 146766] processes coverage from wiggle files and does automatic category discovery
urn:lsid:broadinstitute.org:cancer.genome.analysis:00188:77
| coverage_prepare_file | LAML.coverage.prepare.txt |
| patient_list | LAML.patients.txt |
| mutation_list | LAML.maf |
| Execution Times: | |
| Submitted: | 16:24:46 16-08-12 |
| Completed: | 17:05:33 16-08-12 |
| Elapsed: | 00 hrs 40 mins 46 secs |
step 3. MutSigRun [id: 146767] perform MutSig calculations, generates output tables and report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:160
| individual_set_id | LAML |
| mutation_file | LAML.maf |
| coverage_file | LAML.coverage.mat |
| patient_file | LAML.patients.txt |
| category_file | LAML.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 | LAML.mutation_preprocessing_report.txt |
| jobcount | 200 |
| Execution Times: | |
| Submitted: | 16:24:46 16-08-12 |
| Completed: | 00:42:27 17-08-12 |
| Elapsed: | 08 hrs 17 mins 41 secs |
step 4. CoMut [id: 146768]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00488:7
| individualSetId | LAML |
| patientCRFile | LAML.patients.counts_and_rates.txt |
| mafFile | LAML.final_analysis_set.maf |
| mutcategsFile | LAML.mutcategs.txt |
| sigGenesFile | LAML.sig_genes.txt |
| Output Files: | |
| LAML_coMut.pdf | |
| LAML_coMut.png | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:24:46 16-08-12 |
| Completed: | 00:43:08 17-08-12 |
| Elapsed: | 08 hrs 18 mins 21 secs |
step 5. GenerateStickFigures [id: 146769]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00497:4
| maf | LAML.final_analysis_set.maf |
| sig_genes | LAML.sig_genes.txt |
| Output Files: | |
| generatedStickFigurePaths.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:24:46 16-08-12 |
| Completed: | 00:43:54 17-08-12 |
| Elapsed: | 08 hrs 19 mins 07 secs |
step 6. GDAC_MutSig_Report [id: 146770] Somatic Mutation Report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00413:16
| bar_plot | LAML.bargraphs.png |
| breakdown_table | LAML.mutation_breakdown.txt |
| categories_table | LAML.mutation_rates.txt |
| coverage png | LAML.covplot.png |
| sig_table | LAML.sig_genes.txt |
| cosmic_table | LAML.cosmic_sig_genes.txt |
| cosmic_table2 | LAML.cosmic_sig_genes2.txt |
| cosmic_muts_table | LAML.cosmic_mutations.txt |
| cluster_table | LAML.clustered_muts.txt |
| geneset_table | LAML.sig_genesets.txt |
| genset_table2 | LAML.sig_genesets_2.txt |
| patients_c_and_r | LAML.patients.counts_and_rates.txt |
| ind_set | LAML |
| mutsig_version | LAML.MutSig_version.txt |
| coMut_plot_png | LAML_coMut.png |
| coMut_plot_pdf | LAML_coMut.pdf |
| stick_figures_path | generatedStickFigurePaths.txt |
| maf_path | LAML.final_analysis_set.maf |
| mut_pre_rep_path | LAML.mutation_preprocessing_report.txt |
| mut_filt_rep_path | LAML.mutation_filtering_report.txt |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:24:46 16-08-12 |
| Completed: | 00:44:56 17-08-12 |
| Elapsed: | 08 hrs 20 mins 09 secs |
