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fh_MutSigPreprocess
-i
LAML
-b
hg18
-t
/xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt
-c
/xchip/cga1/lawrence/db/context65
-cw
no_longer_needed
-cat
4
-maf2
/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis7101405989307899307.att_dependentsValues1267464193924302932.tsv
-maflabel1
Broad
-maflabel2
WashU
-maflabel3
Baylor
-wig2
/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis8605315050491331567.att_dependentsValues8975280109617124929.tsv
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt

               perform_mutsig2_analysis: 1
     use_sample_specific_mutation_rates: 1
        analyze_silent_nonsilent_ratios: 1
                 sig_calculation_method: 'projection'
                           print_report: 0
                  clip_tumor_from_names: 1
                                  build: 'hg18'
             keep_barebones_fields_only: 0
    consolidate_adjacent_muts_threshold: 1
             remove_noncoding_mutations: 1
                    enforce_target_list: 0
                            target_list: [1x64 char]
                     mutation_blacklist: []
                     mutation_whitelist: []

Loading MAFs for WashU
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2802-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2803-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2804-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2805-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2806-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2807-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2808-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2809-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2810-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2811-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2812-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2813-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2814-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2815-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2816-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2817-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2818-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2819-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2820-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2821-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2822-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2823-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2824-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2825-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2826-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2827-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2828-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2829-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2830-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2831-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2832-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2833-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2834-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2835-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2836-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2837-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2838-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2839-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2840-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2841-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2842-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2843-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2844-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2845-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2846-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2847-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2848-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2849-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2850-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2851-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2853-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2854-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2855-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2856-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2857-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2858-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2859-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2860-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2861-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2862-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2863-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2864-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2865-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2866-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2867-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2868-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2869-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2870-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2871-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2872-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2873-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2874-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2875-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2876-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2877-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2878-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2879-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2880-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2881-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2882-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2883-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2884-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2885-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2886-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2887-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2888-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2889-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2890-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2891-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2892-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2893-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2894-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2895-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2896-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2897-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2898-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2899-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2900-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2901-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2903-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2904-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2905-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2906-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2907-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2908-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2909-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2910-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2911-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2912-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2913-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2914-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2915-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2916-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2917-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2918-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2919-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2920-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2921-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2922-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2923-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2924-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2925-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2926-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2927-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2928-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2929-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2930-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2931-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2932-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2933-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2934-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2935-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2936-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2937-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2938-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2939-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2940-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2941-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2942-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2943-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2944-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2945-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2946-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2947-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2948-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2949-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2950-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2952-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2954-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2955-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2956-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2957-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2959-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2963-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2964-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2965-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2966-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2967-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2968-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2969-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2970-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2971-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2972-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2973-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2974-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2976-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2977-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2978-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2979-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2980-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2981-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2982-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2983-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2984-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2985-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2986-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2987-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2988-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2989-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2990-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2991-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2992-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2993-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2994-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2995-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2996-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2997-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2998-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-2999-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3000-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3001-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3002-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3005-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3006-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3007-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3008-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3009-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3011-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/laml/tracerel__illuminaga_dnaseq__genome_wustl_edu__Level_2__Mutation_Calling__maf/genome.wustl.edu_LAML.IlluminaGA_DNASeq.Level_2.2.1.0/TCGA-AB-3012-01.maf.txt
Concatenating structs...

                         BAM_file: [199]
                           Center: [199]
                       Chromosome: [199]
                     End_position: [199]
                   Entrez_Gene_Id: [199]
                      Hugo_Symbol: [199]
           Match_Norm_Seq_Allele1: [199]
           Match_Norm_Seq_Allele2: [199]
    Match_Norm_Validation_Allele1: [199]
    Match_Norm_Validation_Allele2: [199]
      Matched_Norm_Sample_Barcode: [199]
                  Mutation_Status: [199]
                       NCBI_Build: [199]
                 Reference_Allele: [199]
                            Score: [199]
                  Sequence_Source: [199]
                        Sequencer: [199]
                 Sequencing_Phase: [199]
                   Start_position: [199]
                           Strand: [199]
             Tumor_Sample_Barcode: [199]
                Tumor_Seq_Allele1: [199]
                Tumor_Seq_Allele2: [199]
         Tumor_Validation_Allele1: [199]
         Tumor_Validation_Allele2: [199]
                Validation_Method: [199]
                Validation_Status: [199]
           Variant_Classification: [199]
                     Variant_Type: [199]
              Verification_Status: [199]
                   all_domains_WU: [199]
             amino_acid_change_WU: [199]
                    c_position_WU: [199]
               chromosome_name_WU: [199]
                          dataset: [199]
                         dbSNP_RS: [199]
                 dbSNP_Val_Status: [199]
        deletion_substructures_WU: [199]
                        domain_WU: [199]
                     gene_name_WU: [199]
                          patient: [199]
                     reference_WU: [199]
                         start_WU: [199]
                          stop_WU: [199]
                        strand_WU: [199]
              transcript_error_WU: [199]
               transcript_name_WU: [199]
             transcript_source_WU: [199]
            transcript_species_WU: [199]
             transcript_status_WU: [199]
            transcript_version_WU: [199]
                      trv_type_WU: [199]
                          type_WU: [199]
                     ucsc_cons_WU: [199]
                       variant_WU: [199]
                        ----TOTAL: [10945]
Calling preprocess_mutations...
Validation_Status:

      Unknown: [4825]
        Valid: [792]
    ----TOTAL: [5617]
Omitting the following 43 mutations on nonstandard chromosomes:

    NT_113889: [8]
    NT_113901: [5]
    NT_113923: [10]
    NT_113925: [1]
    NT_113927: [1]
    NT_113930: [8]
    NT_113933: [3]
    NT_113949: [2]
    NT_113956: [1]
    NT_113961: [4]
    ----TOTAL: [43]
Removing the following non-coding mutations (based on "type" field):
          RNA: [399]
    ----TOTAL: [399]
Not enforcing any target list.
Collapsing adjacent mutations:

       2 SNPs/Indels to one SNP: [5]
    2 redundant SNPs to one SNP: [1]
                      ----TOTAL: [6]

Genes affected:
        DOCK8: [1]
        FRG1B: [1]
       HNRNPK: [1]
         NFE2: [1]
        RAD21: [1]
         TET2: [1]
    ----TOTAL: [6]

Patients affected:
    LAML-AB-2849: [1]
    LAML-AB-2886: [1]
    LAML-AB-2921: [1]
    LAML-AB-2930: [1]
    LAML-AB-2937: [1]
    LAML-AB-2964: [1]
       ----TOTAL: [6]
Collapsed 5175 muts to 5169 muts
get_context: assuming human
Getting context: 43/5169 values in FWB were undefined (-1): these have been changed to NaN in the returned array.

Done.
Saved LAML.mutation_preprocessing_report.txt
Saved LAML.maf
Total of 199 patients had both MAF and WIG data.
Saved LAML.patients.txt
Saved LAML.coverage.prepare.txt
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.84.3413/
LD_LIBRARY_PATH is .:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/runtime/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/bin/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/os/glnxa64:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/server:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64/client:/broad/software/nonfree/Linux/redhat_5_x86_64/pkgs/matlab_2009a/sys/java/jre/glnxa64/jre/lib/amd64
MCR_CACHE_ROOT is  /xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/130521
mFile: fh_MutSigPreprocess
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.84.3413/fh_MutSigPreprocess -i LAML -b hg18 -t /xchip/cga1/lawrence/capture/RefSeq_exons_hg18_june2010_fix1.txt -c /xchip/cga1/lawrence/db/context65 -cw no_longer_needed -cat 4 -maf2 /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis7101405989307899307.att_dependentsValues1267464193924302932.tsv -maflabel1 Broad -maflabel2 WashU -maflabel3 Baylor -wig2 /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/temp/attachments/cgaadm_deadline/Axis8605315050491331567.att_dependentsValues8975280109617124929.tsv -p /xchip/cga1/reference/mutsig_params/MutSig2.0.params.txt
