| Gistic2_Analysis1 seg_file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LIHC/1551569/2.GDAC_MergeDataFiles.Finished/LIHC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt |
| Gistic2_Analysis1 markers_file | file:/xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt |
| Gistic2_Analysis1 refgene_file | file:/xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat |
| Gistic2_Analysis1 cnv_files | /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.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: | 13:54:07 05-08-12 |
| Completed: | |
| Elapsed: | 00 hrs 32 mins 18 secs |
step 1. Gistic2_Analysis [id: 142854] Wrapper module for Gistic v2 (Note: uses segarray to reduce memory)
urn:lsid:broadinstitute.org:cancer.genome.analysis:00264:104
| seg_file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LIHC/1551569/2.GDAC_MergeDataFiles.Finished/LIHC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt |
| markers_file | file:/xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt |
| refgene_file | file:/xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat |
| cnv_files | /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.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: | 13:54:07 05-08-12 |
| Completed: | 14:25:38 05-08-12 |
| Elapsed: | 00 hrs 31 mins 31 secs |
step 2. GDAC_Gistic2Report [id: 142855] Gistic2 results report
urn:lsid:broadinstitute.org:cancer.genome.analysis:00269:47
| 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 |
| gisticInputs txt | gisticInputs.txt |
| Output Files: | |
| hg19_with_miR_20120227.mat | |
| CNV.hg19.bypos.111213.txt | |
| genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 13:54:07 05-08-12 |
| Completed: | 14:26:24 05-08-12 |
| Elapsed: | 00 hrs 32 mins 17 secs |
