| Gistic2_Analysis1 seg_file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COADREAD/1035459/1.GDAC_MergeDataFiles.Finished/COADREAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt |
| Gistic2_Analysis1 markers_file | file:/xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt |
| Gistic2_Analysis1 refgene_file | file:/xchip/cga/reference/gistic/hg18_with_miR_20091116.mat |
| Gistic2_Analysis1 cnv_files | /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt |
| Gistic2_Analysis1 amp_thresh | 0.30 |
| Gistic2_Analysis1 del_thresh | 0.30 |
| Gistic2_Analysis1 cap | 2.0 |
| Gistic2_Analysis1 broad length cutoff | 0.5 |
| Gistic2_Analysis1 remove X | 1 |
| Gistic2_Analysis1 confidence level | 0.99 |
| Gistic2_Analysis1 join segment size | 10 |
| Gistic2_Analysis1 arm peel | 1 |
| Gistic2_Analysis1 max sample segs | 10000 |
| Execution Times: | |
| Submitted: | 04:25:28 29-03-12 |
| Completed: | |
| Elapsed: | 01 hrs 17 mins 08 secs |
step 1. Gistic2_Analysis [id: 68367] Wrapper module for Gistic v2 (Note: uses segarray to reduce memory)
urn:lsid:broadinstitute.org:cancer.genome.analysis:00264:102
| seg_file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/COADREAD/1035459/1.GDAC_MergeDataFiles.Finished/COADREAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_cna__seg.seg.txt |
| markers_file | file:/xchip/tcga/CancerGenomeAnalysisData/trunk/markerfiles/gistic_ovarian/broad.probes.txt |
| refgene_file | file:/xchip/cga/reference/gistic/hg18_with_miR_20091116.mat |
| cnv_files | /xchip/cga/reference/gistic2/pan_TCGA_blood_uber_filter_list.Jan-07-2011.txt,/xchip/cga/reference/gistic2/xchip_tcga_gbm_analysis_mokelly_080429_convert_CNV_to_BED__CNV.verified_080606.combined.txt |
| amp_thresh | 0.30 |
| del_thresh | 0.30 |
| cap | 2.0 |
| broad length cutoff | 0.5 |
| remove X | 1 |
| confidence level | 0.99 |
| join segment size | 10 |
| arm peel | 1 |
| max sample segs | 10000 |
| Execution Times: | |
| Submitted: | 04:25:28 29-03-12 |
| Completed: | 05:41:59 29-03-12 |
| Elapsed: | 01 hrs 16 mins 30 secs |
step 2. GDAC_Gistic2Report [id: 68368] Gistic2 results report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00269:41
| amp | amp_genes.conf_99.txt |
| del | del_genes.conf_99.txt |
| amplification png | amp_qplot.png |
| deletion png | del_qplot.png |
| segmented_copy_number png | raw_copy_number.png |
| gistic_version txt | gisticVersion.txt |
| arraylistfile txt | arraylistfile.txt |
| broad_sig_res | broad_significance_results.txt |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 04:25:28 29-03-12 |
| Completed: | 05:42:34 29-03-12 |
| Elapsed: | 01 hrs 17 mins 05 secs |
