| MutSigPreprocess1 individual_set_id | COADREAD |
| MutSigPreprocess1 maf1 | dependentsValues2711467218948810909.tsv |
| MutSigPreprocess1 maf3 | dependentsValues8364190190982078358.tsv |
| MutSigPreprocess1 maflabel1 | Broad |
| MutSigPreprocess1 maflabel2 | WashU |
| MutSigPreprocess1 maflabel3 | Baylor |
| MutSigPreprocess1 wig1 | dependentsValues962128363007749436.tsv |
| MutSigPreprocess1 wig3 | dependentsValues1010758032101399239.tsv |
| MutSigPreprocess1 build | hg18 |
| MutSigPreprocess1 context65_dir | /xchip/cga1/lawrence/db/context65 |
| MutSigPreprocess1 context65_wig | no_longer_needed |
| 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 genome_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_Report5 ind_set | COADREAD |
| Execution Times: | |
| Submitted: | 19:22:13 12-07-12 |
| Completed: | |
| Elapsed: | 12 hrs 14 mins 21 secs |
step 1. MutSigPreprocess [id: 126338] preprocess patient list and mutations
urn:lsid:broadinstitute.org:cancer.genome.analysis:00272:84
| individual_set_id | COADREAD |
| maf1 | dependentsValues2711467218948810909.tsv |
| maf2 | |
| maf3 | dependentsValues8364190190982078358.tsv |
| maf4 | |
| maflabel1 | Broad |
| maflabel2 | WashU |
| maflabel3 | Baylor |
| maflabel4 | |
| wig1 | dependentsValues962128363007749436.tsv |
| wig2 | |
| wig3 | dependentsValues1010758032101399239.tsv |
| wig4 | |
| build | hg18 |
| context65_dir | /xchip/cga1/lawrence/db/context65 |
| context65_wig | no_longer_needed |
| 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.coverage.prepare.txt | |
| COADREAD.patients.txt | |
| COADREAD.maf | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 19:22:13 12-07-12 |
| Completed: | 19:25:04 12-07-12 |
| Elapsed: | 00 hrs 02 mins 50 secs |
step 2. ProcessCoverageForMutSig [id: 126339] processes coverage from wiggle files and does automatic category discovery
urn:lsid:broadinstitute.org:cancer.genome.analysis:00188:72
| coverage_prepare_file | COADREAD.coverage.prepare.txt |
| patient_list | COADREAD.patients.txt |
| mutation_list | COADREAD.maf |
| Execution Times: | |
| Submitted: | 19:22:13 12-07-12 |
| Completed: | 19:43:21 12-07-12 |
| Elapsed: | 00 hrs 21 mins 07 secs |
step 3. MutSigRun [id: 126340] perform MutSig calculations, generates output tables and report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00286:153
| 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 |
| genome_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: | 19:22:13 12-07-12 |
| Completed: | 07:35:32 13-07-12 |
| Elapsed: | 12 hrs 13 mins 18 secs |
step 4. CoMut [id: 126341]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00488:4
| 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: | 19:22:13 12-07-12 |
| Completed: | 07:36:17 13-07-12 |
| Elapsed: | 12 hrs 14 mins 03 secs |
step 5. GDAC_MutSig_Report [id: 126342] Somatic Mutation Report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00413:13
| 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 |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 19:22:13 12-07-12 |
| Completed: | 07:36:32 13-07-12 |
| Elapsed: | 12 hrs 14 mins 19 secs |
