| MutSigPreprocess1 individual_set_id | BRCA |
| MutSigPreprocess1 maf2 | MutSigPreprocess1.maf2.input.tsv |
| MutSigPreprocess1 maflabel1 | Broad |
| MutSigPreprocess1 maflabel2 | WashU |
| MutSigPreprocess1 maflabel3 | Baylor |
| MutSigPreprocess1 wig2 | MutSigPreprocess1.wig2.input.tsv |
| MutSigPreprocess1 build | hg19 |
| MutSigPreprocess1 context65_dir | /xchip/cga1/annotation/db/tracks/hg19/c65e |
| MutSigPreprocess1 build_dir | /xchip/cga1/annotation/db/ucsc/hg19 |
| MutSigPreprocess1 num_categories | 4 |
| MutSigPreprocess1 target_list | /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt |
| MutSigPreprocess1 paramfile | /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt |
| MutSigRun3 individual_set_id | BRCA |
| MutSigRun3 gene_list | /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt |
| MutSigRun3 build | hg19 |
| 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/hg19/R.mat |
| MutSigRun3 build_dir | /xchip/cga1/annotation/db/ucsc/hg19 |
| MutSigRun3 param_file | /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt |
| MutSigRun3 jobcount | 200 |
| CoMut4 individualSetId | BRCA |
| GDAC_MutSig_Report6 ind_set | BRCA |
| Execution Times: | |
| Submitted: | 16:21:46 16-08-12 |
| Completed: | |
| Elapsed: | 15 hrs 40 mins 59 secs |
step 1. MutSigPreprocess [id: 146737] preprocess patient list and mutations
urn:lsid:broadinstitute.org:cancer.genome.analysis:00272:90
| individual_set_id | BRCA |
| maf1 | |
| maf2 | MutSigPreprocess1.maf2.input.tsv |
| maf3 | |
| maf4 | |
| maflabel1 | Broad |
| maflabel2 | WashU |
| maflabel3 | Baylor |
| maflabel4 | |
| wig1 | |
| wig2 | MutSigPreprocess1.wig2.input.tsv |
| wig3 | |
| wig4 | |
| build | hg19 |
| context65_dir | /xchip/cga1/annotation/db/tracks/hg19/c65e |
| build_dir | /xchip/cga1/annotation/db/ucsc/hg19 |
| num_categories | 4 |
| target_list | /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt |
| paramfile | /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt |
| Output Files: | |
| BRCA.mutation_preprocessing_report.txt | |
| BRCA.maf | |
| BRCA.coverage.prepare.txt | |
| BRCA.patients.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:21:46 16-08-12 |
| Completed: | 16:24:04 16-08-12 |
| Elapsed: | 00 hrs 02 mins 17 secs |
step 2. ProcessCoverageForMutSig [id: 146738] processes coverage from wiggle files and does automatic category discovery
urn:lsid:broadinstitute.org:cancer.genome.analysis:00188:77
| coverage_prepare_file | BRCA.coverage.prepare.txt |
| patient_list | BRCA.patients.txt |
| mutation_list | BRCA.maf |
| Execution Times: | |
| Submitted: | 16:21:47 16-08-12 |
| Completed: | 19:29:48 16-08-12 |
| Elapsed: | 03 hrs 08 mins 01 secs |
step 3. MutSigRun [id: 146739] perform MutSig calculations, generates output tables and report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:160
| individual_set_id | BRCA |
| mutation_file | BRCA.maf |
| coverage_file | BRCA.coverage.mat |
| patient_file | BRCA.patients.txt |
| category_file | BRCA.mutcategs.txt |
| gene_list | /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_genelist.txt |
| build | hg19 |
| 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/hg19/R.mat |
| build_dir | /xchip/cga1/annotation/db/ucsc/hg19 |
| param_file | /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt |
| mutation_preprocessing_report_file | BRCA.mutation_preprocessing_report.txt |
| jobcount | 200 |
| Execution Times: | |
| Submitted: | 16:21:47 16-08-12 |
| Completed: | 08:00:26 17-08-12 |
| Elapsed: | 15 hrs 38 mins 39 secs |
step 4. CoMut [id: 146740]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00488:7
| individualSetId | BRCA |
| patientCRFile | BRCA.patients.counts_and_rates.txt |
| mafFile | BRCA.final_analysis_set.maf |
| mutcategsFile | BRCA.mutcategs.txt |
| sigGenesFile | BRCA.sig_genes.txt |
| Output Files: | |
| BRCA_coMut.pdf | |
| BRCA_coMut.png | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:21:47 16-08-12 |
| Completed: | 08:01:27 17-08-12 |
| Elapsed: | 15 hrs 39 mins 40 secs |
step 5. GenerateStickFigures [id: 146741]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00497:4
| maf | BRCA.final_analysis_set.maf |
| sig_genes | BRCA.sig_genes.txt |
| Output Files: | |
| generatedStickFigurePaths.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:21:47 16-08-12 |
| Completed: | 08:01:58 17-08-12 |
| Elapsed: | 15 hrs 40 mins 11 secs |
step 6. GDAC_MutSig_Report [id: 146742] Somatic Mutation Report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00413:16
| bar_plot | BRCA.bargraphs.png |
| breakdown_table | BRCA.mutation_breakdown.txt |
| categories_table | BRCA.mutation_rates.txt |
| coverage png | BRCA.covplot.png |
| sig_table | BRCA.sig_genes.txt |
| cosmic_table | BRCA.cosmic_sig_genes.txt |
| cosmic_table2 | BRCA.cosmic_sig_genes2.txt |
| cosmic_muts_table | BRCA.cosmic_mutations.txt |
| cluster_table | BRCA.clustered_muts.txt |
| geneset_table | BRCA.sig_genesets.txt |
| genset_table2 | BRCA.sig_genesets_2.txt |
| patients_c_and_r | BRCA.patients.counts_and_rates.txt |
| ind_set | BRCA |
| mutsig_version | BRCA.MutSig_version.txt |
| coMut_plot_png | BRCA_coMut.png |
| coMut_plot_pdf | BRCA_coMut.pdf |
| stick_figures_path | generatedStickFigurePaths.txt |
| maf_path | BRCA.final_analysis_set.maf |
| mut_pre_rep_path | BRCA.mutation_preprocessing_report.txt |
| mut_filt_rep_path | BRCA.mutation_filtering_report.txt |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:21:47 16-08-12 |
| Completed: | 08:02:44 17-08-12 |
| Elapsed: | 15 hrs 40 mins 57 secs |
