| cnvarms2cluster1 sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/LUSC/1798102/1.Gistic2_Analysis.Finished/broad_values_by_arm.txt |
| Correlate_Clinical_Cnvsarms_onlysig2 clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC/1709126/1.GDAC_clinicalDataPicker.Finished/LUSC.clin.merged.picked.txt |
| Correlate_Clinical_Cnvsarms_onlysig2 filter cluster smaller than | 3 |
| Correlate_Clinical_Cnvsarms_onlysig2 output name | LUSC |
| Correlate_Clinical_Cnvsarms_onlysig2 figure height | 5 |
| Correlate_Clinical_Cnvsarms_onlysig2 figure width | 9 |
| Correlate_Clinical_Cnvsarms_onlysig2 survival legend position | OUT |
| Correlate_Clinical_Cnvsarms_onlysig2 pvalue cutoff | 1 |
| Correlate_Clinical_Cnvsarms_onlysig2 qvalue cutoff | 0.25 |
| Correlate_Clinical_Cnvsarms_onlysig2 make figure | ONLYSIG |
| Correlate_Clinical_Cnvsarms_onlysig2 nozzle ver | Nozzle.R1 |
| Execution Times: | |
| Submitted: | 10:55:49 10-10-12 |
| Completed: | |
| Elapsed: | 00 hrs 02 mins 40 secs |
step 1. cnvarms2cluster [id: 181834] Convert mutsig results to cluster files
urn:lsid:broadinstitute.org:cancer.genome.analysis:00499:3
| sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Pipeline/LUSC/1798102/1.Gistic2_Analysis.Finished/broad_values_by_arm.txt |
| maf file | |
| sig gene file | |
| sig gene q cutoff | 0.01 |
| output name |
| Output Files: | |
| broad_values_by_arm.mutsig.cluster.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 10:56:10 10-10-12 |
| Completed: | 10:57:29 10-10-12 |
| Elapsed: | 00 hrs 01 mins 19 secs |
step 2. Correlate_Clinical_Cnvsarms_onlysig [id: 181835]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00498:11
| cluster label file | broad_values_by_arm.mutsig.cluster.txt |
| clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LUSC/1709126/1.GDAC_clinicalDataPicker.Finished/LUSC.clin.merged.picked.txt |
| features used | ALL |
| filter cluster smaller than | 3 |
| output name | LUSC |
| 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 |
| Execution Times: | |
| Submitted: | 10:56:10 10-10-12 |
| Completed: | 10:58:29 10-10-12 |
| Elapsed: | 00 hrs 02 mins 19 secs |