| MutSigPreprocess1 individual_set_id | COADREAD |
| MutSigPreprocess1 maf1 | MutSigPreprocess1.maf1.input.tsv |
| MutSigPreprocess1 maf3 | MutSigPreprocess1.maf3.input.tsv |
| MutSigPreprocess1 maflabel1 | Broad |
| MutSigPreprocess1 maflabel2 | WashU |
| MutSigPreprocess1 maflabel3 | Baylor |
| MutSigPreprocess1 wig1 | MutSigPreprocess1.wig1.input.tsv |
| MutSigPreprocess1 wig3 | MutSigPreprocess1.wig3.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 | COADREAD |
| 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 | COADREAD |
| GDAC_MutSig_Report6 ind_set | COADREAD |
| Execution Times: | |
| Submitted: | 14:04:42 29-08-12 |
| Completed: | |
| Elapsed: | 13 hrs 30 mins 37 secs |
step 1. MutSigPreprocess [id: 160040] preprocess patient list and mutations
urn:lsid:broadinstitute.org:cancer.genome.analysis:00272:90
| individual_set_id | COADREAD |
| maf1 | MutSigPreprocess1.maf1.input.tsv |
| maf2 | |
| maf3 | MutSigPreprocess1.maf3.input.tsv |
| maf4 | |
| maflabel1 | Broad |
| maflabel2 | WashU |
| maflabel3 | Baylor |
| maflabel4 | |
| wig1 | MutSigPreprocess1.wig1.input.tsv |
| wig2 | |
| wig3 | MutSigPreprocess1.wig3.input.tsv |
| 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: | |
| COADREAD.mutation_preprocessing_report.txt | |
| COADREAD.maf | |
| COADREAD.coverage.prepare.txt | |
| COADREAD.patients.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 14:04:42 29-08-12 |
| Completed: | 14:14:38 29-08-12 |
| Elapsed: | 00 hrs 09 mins 55 secs |
step 2. ProcessCoverageForMutSig [id: 160041] processes coverage from wiggle files and does automatic category discovery
urn:lsid:broadinstitute.org:cancer.genome.analysis:00188:77
| coverage_prepare_file | COADREAD.coverage.prepare.txt |
| patient_list | COADREAD.patients.txt |
| mutation_list | COADREAD.maf |
| Execution Times: | |
| Submitted: | 14:04:42 29-08-12 |
| Completed: | 14:48:12 29-08-12 |
| Elapsed: | 00 hrs 43 mins 29 secs |
step 3. MutSigRun [id: 160042] perform MutSig calculations, generates output tables and report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:160
| individual_set_id | COADREAD |
| mutation_file | COADREAD.maf |
| coverage_file | COADREAD.coverage.mat |
| patient_file | COADREAD.patients.txt |
| category_file | COADREAD.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 | COADREAD.mutation_preprocessing_report.txt |
| jobcount | 200 |
| Execution Times: | |
| Submitted: | 14:04:42 29-08-12 |
| Completed: | 03:33:30 30-08-12 |
| Elapsed: | 13 hrs 28 mins 47 secs |
step 4. CoMut [id: 160043]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00488:7
| individualSetId | COADREAD |
| patientCRFile | COADREAD.patients.counts_and_rates.txt |
| mafFile | COADREAD.final_analysis_set.maf |
| mutcategsFile | COADREAD.mutcategs.txt |
| sigGenesFile | COADREAD.sig_genes.txt |
| Output Files: | |
| COADREAD_coMut.pdf | |
| COADREAD_coMut.png | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 14:04:42 29-08-12 |
| Completed: | 03:34:15 30-08-12 |
| Elapsed: | 13 hrs 29 mins 32 secs |
step 5. GenerateStickFigures [id: 160044]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00497:4
| maf | COADREAD.final_analysis_set.maf |
| sig_genes | COADREAD.sig_genes.txt |
| Output Files: | |
| generatedStickFigurePaths.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 14:04:42 29-08-12 |
| Completed: | 03:34:46 30-08-12 |
| Elapsed: | 13 hrs 30 mins 03 secs |
step 6. GDAC_MutSig_Report [id: 160045] Somatic Mutation Report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00413:16
| bar_plot | COADREAD.bargraphs.png |
| breakdown_table | COADREAD.mutation_breakdown.txt |
| categories_table | COADREAD.mutation_rates.txt |
| coverage png | COADREAD.covplot.png |
| sig_table | COADREAD.sig_genes.txt |
| cosmic_table | COADREAD.cosmic_sig_genes.txt |
| cosmic_table2 | COADREAD.cosmic_sig_genes2.txt |
| cosmic_muts_table | COADREAD.cosmic_mutations.txt |
| cluster_table | COADREAD.clustered_muts.txt |
| geneset_table | COADREAD.sig_genesets.txt |
| genset_table2 | COADREAD.sig_genesets_2.txt |
| patients_c_and_r | COADREAD.patients.counts_and_rates.txt |
| ind_set | COADREAD |
| mutsig_version | COADREAD.MutSig_version.txt |
| coMut_plot_png | COADREAD_coMut.png |
| coMut_plot_pdf | COADREAD_coMut.pdf |
| stick_figures_path | generatedStickFigurePaths.txt |
| maf_path | COADREAD.final_analysis_set.maf |
| mut_pre_rep_path | COADREAD.mutation_preprocessing_report.txt |
| mut_filt_rep_path | COADREAD.mutation_filtering_report.txt |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 14:04:42 29-08-12 |
| Completed: | 03:35:17 30-08-12 |
| Elapsed: | 13 hrs 30 mins 34 secs |
