| cnv2cluster1 sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/BRCA/1795484/1.Gistic2_Analysis.Finished/all_lesions.conf_99.txt |
| Correlate_Clinical_Cnvs_onlysig2 clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BRCA/1708556/1.GDAC_clinicalDataPicker.Finished/BRCA.clin.merged.picked.txt |
| Correlate_Clinical_Cnvs_onlysig2 filter cluster smaller than | 3 |
| Correlate_Clinical_Cnvs_onlysig2 output name | BRCA |
| Correlate_Clinical_Cnvs_onlysig2 figure height | 5 |
| Correlate_Clinical_Cnvs_onlysig2 figure width | 9 |
| Correlate_Clinical_Cnvs_onlysig2 survival legend position | OUT |
| Correlate_Clinical_Cnvs_onlysig2 pvalue cutoff | 1 |
| Correlate_Clinical_Cnvs_onlysig2 qvalue cutoff | 0.25 |
| Correlate_Clinical_Cnvs_onlysig2 make figure | ONLYSIG |
| Correlate_Clinical_Cnvs_onlysig2 nozzle ver | Nozzle.R1 |
| Execution Times: | |
| Submitted: | 09:01:50 10-10-12 |
| Completed: | |
| Elapsed: | 00 hrs 01 mins 33 secs |
step 1. cnv2cluster [id: 181488] Convert mutsig results to cluster files
urn:lsid:broadinstitute.org:cancer.genome.analysis:00494:12
| sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/BRCA/1795484/1.Gistic2_Analysis.Finished/all_lesions.conf_99.txt |
| maf file | |
| sig gene file | |
| sig gene q cutoff | 0.01 |
| output name |
| Output Files: | |
| all_lesions.conf_99.cnv.cluster.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 09:01:56 10-10-12 |
| Completed: | 09:02:19 10-10-12 |
| Elapsed: | 00 hrs 00 mins 22 secs |
step 2. Correlate_Clinical_Cnvs_onlysig [id: 181489]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00495:41
| cluster label file | all_lesions.conf_99.cnv.cluster.txt |
| clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/BRCA/1708556/1.GDAC_clinicalDataPicker.Finished/BRCA.clin.merged.picked.txt |
| features used | ALL |
| filter cluster smaller than | 3 |
| output name | BRCA |
| figure height | 5 |
| figure width | 9 |
| survival legend position | OUT |
| pvalue cutoff | 1 |
| qvalue cutoff | 0.25 |
| make figure | ONLYSIG |
| nozzle ver | Nozzle.R1 |
| options | MUTSIG |
| report title | |
| job description |
| Output Files: | |
| D25V3.pdf | |
| D25V3.png | |
| D32V2.pdf | |
| D32V2.png | |
| D39V2.png | |
| D39V2.pdf | |
| D45V5.pdf | |
| D45V5.png | |
| D58V2.pdf | |
| D58V2.png | |
| table.1.txt | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 09:01:56 10-10-12 |
| Completed: | 09:03:22 10-10-12 |
| Elapsed: | 00 hrs 01 mins 26 secs |