Warning: No display specified.  You will not be able to display graphics on the screen.
fh_MutSigPreprocess
libdir = /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.90.3705/
-i
KIRP-TP
-b
hg19
-t
/xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt
-c
/xchip/cga1/annotation/db/tracks/hg19/c65e
-bd
/xchip/cga1/annotation/db/ucsc/hg19
-cat
4
-maf1
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/KIRP-TP/2283891/maf1.input.tsv
-maflabel1
Broad
-maflabel2
WashU
-maflabel3
Baylor
-wig1
/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/KIRP-TP/2283891/wig1.input.tsv
-p
/xchip/cga1/reference/mutsig_params/MutSig2.0_cga.pancan.blacklist.v7.hg19.params.txt

                     mutation_blacklist: [1x73 char]
               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: 'hg19'
                              build_dir: '/xchip/cga1/annotation/db/ucsc/hg19'
             keep_barebones_fields_only: 0
    consolidate_adjacent_muts_threshold: 1
             remove_noncoding_mutations: 1
                    enforce_target_list: 0
                            target_list: [1x69 char]
                     mutation_whitelist: []

Loading MAFs for Broad
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7286-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7287-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7288-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7583-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7584-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7585-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7732-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7734-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7828-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7915-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7996-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-A4-7997-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-3466-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-3467-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-3468-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-3472-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-3473-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-AL-7173-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B1-5398-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B3-3925-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B3-3926-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B3-4103-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B3-4104-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4113-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4114-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4115-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4116-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4117-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-4617-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-5155-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-5156-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-B9-7268-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5875-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5876-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5877-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5878-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5879-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5880-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5881-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5882-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5883-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5884-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5885-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5886-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5887-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5888-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5889-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5890-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5891-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5892-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5893-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-5894-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7044-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7045-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7046-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7048-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7049-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7050-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7051-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7053-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7055-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7056-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7058-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7059-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7060-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7061-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-BQ-7062-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-5560-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-5561-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7834-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7837-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7838-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7839-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7840-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7841-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DW-7842-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DZ-6131-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DZ-6132-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DZ-6133-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DZ-6134-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-DZ-6135-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EV-5901-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EV-5902-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-EV-5903-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6789-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6790-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6792-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6793-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6795-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6796-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-6797-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-7501-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-G7-7502-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-GL-6846-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-GL-7773-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-GL-7966-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-HE-7128-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-HE-7129-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-HE-7130-01.maf.txt
Loaded /xchip/gdac_data/normalized/diced/kirp/tracerel__illuminaga_dnaseq__broad_mit_edu__Level_2__Mutation_Calling__maf/broad.mit.edu_KIRP.IlluminaGA_DNASeq.Level_2.2.0.0/TCGA-J7-6720-01.maf.txt
Concatenating structs...

                   Annotation_Transcript: [100]
                                BAM_file: [100]
      CCLE_ONCOMAP_overlapping_mutations: [100]
    CCLE_ONCOMAP_total_mutations_in_gene: [100]
                       CGC_Mutation_Type: [100]
                      CGC_Other_Diseases: [100]
               CGC_Translocation_Partner: [100]
                CGC_Tumor_Types_Germline: [100]
                 CGC_Tumor_Types_Somatic: [100]
                     COSMIC_fusion_genes: [100]
            COSMIC_overlapping_mutations: [100]
            COSMIC_tissue_types_affected: [100]
        COSMIC_total_alterations_in_gene: [100]
                                  Center: [100]
                              Chromosome: [100]
                            Codon_Change: [100]
                     DNARepairGenes_Role: [100]
                             Description: [100]
                                DrugBank: [100]
                            End_position: [100]
                          Entrez_Gene_Id: [100]
        FamilialCancerDatabase_Syndromes: [100]
                   GO_Biological_Process: [100]
                   GO_Cellular_Component: [100]
                   GO_Molecular_Function: [100]
                           Genome_Change: [100]
                             Hugo_Symbol: [100]
                MUTSIG_Published_Results: [100]
                  Match_Norm_Seq_Allele1: [100]
                  Match_Norm_Seq_Allele2: [100]
           Match_Norm_Validation_Allele1: [100]
           Match_Norm_Validation_Allele2: [100]
             Matched_Norm_Sample_Barcode: [100]
                Matched_Norm_Sample_UUID: [100]
                         Mutation_Status: [100]
                              NCBI_Build: [100]
                             OREGANNO_ID: [100]
                         OREGANNO_Values: [100]
                       Other_Transcripts: [100]
                          Protein_Change: [100]
                        Reference_Allele: [100]
                          Refseq_mRNA_Id: [100]
                          Refseq_prot_Id: [100]
                                   Score: [100]
                         Sequence_Source: [100]
                               Sequencer: [100]
                        Sequencing_Phase: [100]
                          Start_position: [100]
                                  Strand: [100]
                        SwissProt_acc_Id: [100]
                      SwissProt_entry_Id: [100]
           TCGAscape_Amplification_Peaks: [100]
                TCGAscape_Deletion_Peaks: [100]
                         Transcript_Exon: [100]
                     Transcript_Position: [100]
                       Transcript_Strand: [100]
                    Tumor_Sample_Barcode: [100]
                       Tumor_Sample_UUID: [100]
                       Tumor_Seq_Allele1: [100]
                       Tumor_Seq_Allele2: [100]
                Tumor_Validation_Allele1: [100]
                Tumor_Validation_Allele2: [100]
          Tumorscape_Amplification_Peaks: [100]
               Tumorscape_Deletion_Peaks: [100]
                           UniProt_AApos: [100]
               UniProt_Experimental_Info: [100]
              UniProt_Natural_Variations: [100]
                          UniProt_Region: [100]
                            UniProt_Site: [100]
                       Validation_Method: [100]
                       Validation_Status: [100]
                  Variant_Classification: [100]
                            Variant_Type: [100]
                     Verification_Status: [100]
                             cDNA_Change: [100]
                                 dataset: [100]
                                dbSNP_RS: [100]
                        dbSNP_Val_Status: [100]
                              gc_content: [100]
                          isArtifactMode: [100]
                                 oxoGCut: [100]
                                 patient: [100]
                                     pox: [100]
                              pox_cutoff: [100]
                                     qox: [100]
                             ref_context: [100]
                             t_alt_count: [100]
                             t_ref_count: [100]
                   validation_alt_allele: [100]
                       validation_method: [100]
                       validation_status: [100]
                 validation_tumor_sample: [100]
                               ----TOTAL: [9200]
Calling preprocess_mutations...
WARNING: unknown chromosome(s):
    'M'
    'MT'

Validation_Status:

             : [9057]
    ----TOTAL: [9057]
Omitting the following 42 mutations on nonstandard chromosomes:

            M: [10]
           MT: [32]
    ----TOTAL: [42]
Applying mutation blacklist:  /xchip/cga1/reference/mutsig_params/pancan_mutation_blacklist.v7.hg19.txt
WARNING: unknown chromosome(s):
    {''}

WARNING: chromosome number(s) out of range for this genome
     0

{Warning: The KEYBOARD function cannot be used in compiled applications.} 
> In keyboard at 4
  In convert_chr at 104
  In add_and_convert_simple_fieldnames at 32
  In preprocess_mutations at 77
  In fh_MutSigPreprocess at 200
Omitting the following 318 blacklisted mutations:
  Columns 1 through 4

    'KIRP-A4-7286-TP'    'KRTAP4-11'       [17]    [ 39274291]
    'KIRP-A4-7286-TP'    'ANKRD32'         [ 5]    [ 94030836]
    'KIRP-A4-7286-TP'    'APOB'            [ 2]    [ 21266775]
    'KIRP-A4-7288-TP'    'UNC93B1'         [11]    [ 67759236]
    'KIRP-A4-7288-TP'    'Unknown'         [16]    [ 70268158]
    'KIRP-A4-7288-TP'    'ZNF814'          [19]    [ 58385762]
    'KIRP-A4-7583-TP'    'ANKRD32'         [ 5]    [ 94030836]
    'KIRP-A4-7585-TP'    'STAG3L2'         [ 7]    [ 74300557]
    'KIRP-A4-7732-TP'    'FRG1B'           [20]    [ 29628245]
    'KIRP-A4-7732-TP'    'TUBBP5'          [ 9]    [141071110]
    'KIRP-A4-7734-TP'    'FAT3'            [11]    [ 92616488]
    'KIRP-A4-7734-TP'    'H1FOO'           [ 3]    [129268107]
    'KIRP-A4-7828-TP'    'MAP3K9'          [14]    [ 71275774]
    'KIRP-A4-7828-TP'    'HCG4'            [ 6]    [ 29760353]
    'KIRP-A4-7915-TP'    'RRN3P1'          [16]    [ 21817457]
    'KIRP-A4-7997-TP'    'Unknown'         [15]    [102292770]
    'KIRP-A4-7997-TP'    'Unknown'         [11]    [ 43283606]
    'KIRP-A4-7997-TP'    'PODXL'           [ 7]    [131241030]
    'KIRP-AL-3466-TP'    'LOC645752'       [15]    [ 78211548]
    'KIRP-AL-3467-TP'    'TPTE'            [21]    [ 11014952]
    'KIRP-AL-3468-TP'    'Unknown'         [12]    [    92000]
    'KIRP-AL-3468-TP'    'POLR3B'          [12]    [106820975]
    'KIRP-AL-3468-TP'    'MUC4'            [ 3]    [195505813]
    'KIRP-AL-3468-TP'    'FMN2'            [ 1]    [240255569]
    'KIRP-AL-3468-TP'    'PCSK2'           [20]    [ 17207956]
    'KIRP-AL-3472-TP'    'DDX11L2'         [ 2]    [114357557]
    'KIRP-AL-3473-TP'    'FOLH1B'          [11]    [ 89413808]
    'KIRP-AL-3473-TP'    'ARHGAP11B'       [15]    [ 30938483]
    'KIRP-AL-3473-TP'    'POM121L9P'       [22]    [ 24659809]
    'KIRP-AL-3473-TP'    'MUC4'            [ 3]    [195511945]
    'KIRP-AL-3473-TP'    'FLJ10661'        [ 8]    [  8092104]
    'KIRP-AL-3473-TP'    'LOC442421'       [ 9]    [ 66499867]
    'KIRP-AL-7173-TP'    'NBPF1'           [ 1]    [ 16918653]
    'KIRP-AL-7173-TP'    'WASH3P'          [15]    [102515299]
    'KIRP-AL-7173-TP'    'POM121L9P'       [22]    [ 24659591]
    'KIRP-AL-7173-TP'    'POM121L9P'       [22]    [ 24659593]
    'KIRP-B1-5398-TP'    'NBPF1'           [ 1]    [ 16918653]
    'KIRP-B1-5398-TP'    'WASH2P'          [ 2]    [114355129]
    'KIRP-B1-5398-TP'    'TBP'             [ 6]    [170871082]
    'KIRP-B1-5398-TP'    'ADAM6'           [14]    [106774086]
    'KIRP-B3-3925-TP'    'C21orf99'        [21]    [ 14439208]
    'KIRP-B3-3925-TP'    'RRN3P1'          [16]    [ 21817457]
    'KIRP-B3-3925-TP'    'FLJ36000'        [17]    [ 21904204]
    'KIRP-B3-3925-TP'    'Unknown'         [ 2]    [ 96521777]
    'KIRP-B3-3925-TP'    'UPK3A'           [22]    [ 45683306]
    'KIRP-B3-3925-TP'    'MUC4'            [ 3]    [195505836]
    'KIRP-B3-3925-TP'    'KRTAP4-7'        [17]    [ 39240900]
    'KIRP-B3-3925-TP'    'TCF7'            [ 5]    [133451702]
    'KIRP-B3-3925-TP'    'NBPF1'           [ 1]    [ 16918653]
    'KIRP-B3-3925-TP'    'FLJ36000'        [17]    [ 21904204]
    'KIRP-B3-3925-TP'    'ZNF814'          [19]    [ 58385546]
    'KIRP-B3-3925-TP'    'FRG1B'           [20]    [ 29628263]
    'KIRP-B3-3925-TP'    'UPK3A'           [22]    [ 45683306]
    'KIRP-B3-3925-TP'    'MUC4'            [ 3]    [195505838]
    'KIRP-B3-3925-TP'    'Unknown'         [15]    [ 62538522]
    'KIRP-B3-3925-TP'    'POLDIP2'         [17]    [ 26684394]
    'KIRP-B3-3926-TP'    'PARG'            [10]    [ 51093329]
    'KIRP-B3-3926-TP'    'KRTAP5-4'        [11]    [  1643252]
    'KIRP-B3-3926-TP'    'FAM83G'          [17]    [ 18874919]
    'KIRP-B3-3926-TP'    'PBX2'            [ 6]    [ 32155509]
    'KIRP-B3-3926-TP'    'LYPLA2P1'        [ 6]    [ 33333342]
    'KIRP-B3-3926-TP'    'BRSK1'           [19]    [ 55815036]
    'KIRP-B3-4103-TP'    'LOC653544'       [10]    [135491113]
    'KIRP-B3-4103-TP'    'FLJ36000'        [17]    [ 21904114]
    'KIRP-B3-4103-TP'    'SLC1A5'          [19]    [ 47280575]
    'KIRP-B3-4103-TP'    'LRRTM1'          [ 2]    [ 80529414]
    'KIRP-B3-4103-TP'    'MUC4'            [ 3]    [195515463]
    'KIRP-B3-4103-TP'    'ANKRD20B'        [ 2]    [ 95522772]
    'KIRP-B3-4103-TP'    'POU6F2'          [ 7]    [ 39500263]
    'KIRP-B3-4103-TP'    'DDX12'           [12]    [  9573997]
    'KIRP-B3-4103-TP'    'GOLGA6L5'        [15]    [ 85055802]
    'KIRP-B3-4103-TP'    'RRN3P1'          [16]    [ 21817457]
    'KIRP-B3-4103-TP'    'TUBBP5'          [ 9]    [141070111]
    'KIRP-B3-4103-TP'    'RRN3P1'          [16]    [ 21817457]
    'KIRP-B3-4103-TP'    'SDHAP2'          [ 3]    [195400799]
    'KIRP-B3-4103-TP'    'UBXN11'          [ 1]    [ 26608820]
    'KIRP-B3-4103-TP'    'POLDIP2'         [17]    [ 26684394]
    'KIRP-B3-4103-TP'    'PRIM2'           [ 6]    [ 57512916]
    'KIRP-B3-4104-TP'    'ARHGAP22'        [10]    [ 49667829]
    'KIRP-B3-4104-TP'    'LOC645752'       [15]    [ 78211648]
    'KIRP-B3-4104-TP'    'ZNF845'          [19]    [ 53856730]
    'KIRP-B3-4104-TP'    'CROCCL1'         [ 1]    [ 16946407]
    'KIRP-B3-4104-TP'    'Unknown'         [ 1]    [148882025]
    'KIRP-B3-4104-TP'    'ARHGAP22'        [10]    [ 49667829]
    'KIRP-B3-4104-TP'    'Unknown'         [16]    [ 70268158]
    'KIRP-B3-4104-TP'    'ARHGAP22'        [10]    [ 49667829]
    'KIRP-B3-4104-TP'    'MYH7'            [14]    [ 23887583]
    'KIRP-B3-4104-TP'    'LYPLA2P1'        [ 6]    [ 33333342]
    'KIRP-B3-4104-TP'    'CUL7'            [ 6]    [ 43013806]
    'KIRP-B3-4104-TP'    'Unknown'         [ 1]    [148882025]
    'KIRP-B3-4104-TP'    'Unknown'         [10]    [ 48968566]
    'KIRP-B3-4104-TP'    'ARHGAP22'        [10]    [ 49667829]
    'KIRP-B3-4104-TP'    'DHX40P1'         [17]    [ 58066651]
    'KIRP-B3-4104-TP'    'UBXN11'          [ 1]    [ 26608820]
    'KIRP-B3-4104-TP'    'UBXN11'          [ 1]    [ 26608878]
    'KIRP-B3-4104-TP'    'POLDIP2'         [17]    [ 26684394]
    'KIRP-B3-4104-TP'    'AFF3'            [ 2]    [100210335]
    'KIRP-B3-4104-TP'    'ODF1'            [ 8]    [103572984]
    'KIRP-B9-4113-TP'    'ANKRD20B'        [ 2]    [ 95522772]
    'KIRP-B9-4113-TP'    'LOC96610'        [22]    [ 22664606]
    'KIRP-B9-4114-TP'    'CROCCL1'         [ 1]    [ 16946434]
    'KIRP-B9-4114-TP'    'CROCCL1'         [ 1]    [ 16946438]
    'KIRP-B9-4114-TP'    'LOC650368'       [11]    [  3427845]
    'KIRP-B9-4114-TP'    'LOC100133050'    [ 5]    [ 99715528]
    'KIRP-B9-4115-TP'    'RPL13AP20'       [12]    [ 13028751]
    'KIRP-B9-4115-TP'    'ANKRD20B'        [ 2]    [ 95522772]
    'KIRP-B9-4116-TP'    'FMOD'            [ 1]    [203311609]
    'KIRP-B9-4116-TP'    'LOC653544'       [10]    [135491112]
    'KIRP-B9-4116-TP'    'UPF3A'           [13]    [115047559]
    'KIRP-B9-4116-TP'    'Unknown'         [ 2]    [ 96521777]
    'KIRP-B9-4116-TP'    'LOC100133050'    [ 5]    [ 99715528]
    'KIRP-B9-4116-TP'    'Unknown'         [ 9]    [ 68414259]
    'KIRP-B9-4116-TP'    'STAG3L2'         [ 7]    [ 74300557]
    'KIRP-B9-4117-TP'    'Unknown'         [16]    [ 32070612]
    'KIRP-B9-4117-TP'    'LOC96610'        [22]    [ 22661187]
    'KIRP-B9-4117-TP'    'POM121L9P'       [22]    [ 24659809]
    'KIRP-B9-4117-TP'    'MUC4'            [ 3]    [195505836]
    'KIRP-B9-4117-TP'    'PTPN18'          [ 2]    [131129929]
    'KIRP-B9-4117-TP'    'HRCT1'           [ 9]    [ 35906584]
    'KIRP-B9-4117-TP'    'NUDT11'          [23]    [ 51239296]
    'KIRP-B9-4617-TP'    'TUBBP5'          [ 9]    [141071110]
    'KIRP-B9-5155-TP'    'MUC4'            [ 3]    [195508343]
    'KIRP-B9-5156-TP'    'ZNF814'          [19]    [ 58385762]
    'KIRP-B9-5156-TP'    'SCAI'            [ 9]    [127790688]
    'KIRP-B9-7268-TP'    'NBPF1'           [ 1]    [ 16918653]
    'KIRP-B9-7268-TP'    'Unknown'         [16]    [ 15023266]
    'KIRP-B9-7268-TP'    'RPSAP58'         [19]    [ 24010294]
    'KIRP-B9-7268-TP'    'FCGBP'           [19]    [ 40367841]
    'KIRP-B9-7268-TP'    'LOC96610'        [22]    [ 22663086]
    'KIRP-BQ-5875-TP'    'RYR3'            [15]    [ 33962623]
    'KIRP-BQ-5875-TP'    'RRN3'            [16]    [ 15168670]
    'KIRP-BQ-5875-TP'    'KRTAP4-9'        [17]    [ 39262083]
    'KIRP-BQ-5875-TP'    'KRTAP4-9'        [17]    [ 39262103]
    'KIRP-BQ-5875-TP'    'PODXL'           [ 7]    [131241030]
    'KIRP-BQ-5875-TP'    'ODF1'            [ 8]    [103572984]
    'KIRP-BQ-5876-TP'    'MEF2B'           [19]    [ 19258537]
    'KIRP-BQ-5876-TP'    'FOXE1'           [ 9]    [100616701]
    'KIRP-BQ-5877-TP'    'SYN2'            [ 3]    [ 12046124]
    'KIRP-BQ-5878-TP'    'AMOT'            [23]    [112022644]
    'KIRP-BQ-5879-TP'    'UGT2B10'         [ 4]    [ 69870669]
    'KIRP-BQ-5879-TP'    'AR'              [23]    [ 66765161]
    'KIRP-BQ-5879-TP'    'OR2T35'          [ 1]    [248801602]
    'KIRP-BQ-5880-TP'    'FLJ36000'        [17]    [ 21904193]
    'KIRP-BQ-5880-TP'    'LYPLA2P1'        [ 6]    [ 33333333]
    'KIRP-BQ-5881-TP'    'CNTNAP2'         [ 7]    [147183114]
    'KIRP-BQ-5881-TP'    'PLAC4'           [21]    [ 42551272]
    'KIRP-BQ-5882-TP'    'CLN6'            [15]    [ 68510982]
    'KIRP-BQ-5882-TP'    'FRG1B'           [20]    [ 29628236]
    'KIRP-BQ-5882-TP'    'C21orf99'        [21]    [ 14439185]
    'KIRP-BQ-5882-TP'    'C21orf99'        [21]    [ 14439208]
    'KIRP-BQ-5882-TP'    'LOC96610'        [22]    [ 22664606]
    'KIRP-BQ-5882-TP'    'WNT6'            [ 2]    [219724790]
    'KIRP-BQ-5882-TP'    'TMEM60'          [ 7]    [ 77423460]
    'KIRP-BQ-5883-TP'    'C21orf99'        [21]    [ 14439208]
    'KIRP-BQ-5883-TP'    'MLLT3'           [ 9]    [ 20414343]
    'KIRP-BQ-5884-TP'    'WASH3P'          [15]    [102515344]
    'KIRP-BQ-5884-TP'    'LOC100133050'    [ 5]    [ 99715528]
    'KIRP-BQ-5884-TP'    'FOXE1'           [ 9]    [100616701]
    'KIRP-BQ-5885-TP'    'NBPF1'           [ 1]    [ 16918653]
    'KIRP-BQ-5885-TP'    'Unknown'         [16]    [ 15457701]
    'KIRP-BQ-5885-TP'    'KRTAP4-11'       [17]    [ 39274343]
    'KIRP-BQ-5885-TP'    'MUC4'            [ 3]    [195507874]
    'KIRP-BQ-5885-TP'    'KANK3'           [19]    [  8398950]
    'KIRP-BQ-5886-TP'    'FRG1B'           [20]    [ 29625905]
    'KIRP-BQ-5886-TP'    'HCG4'            [ 6]    [ 29760353]
    'KIRP-BQ-5887-TP'    'CDKN2A'          [ 9]    [ 21974720]
    'KIRP-BQ-5888-TP'    'PLAC4'           [21]    [ 42551272]
    'KIRP-BQ-5889-TP'    'SPDYE7P'         [ 7]    [ 72339497]
    'KIRP-BQ-5892-TP'    'LOC645752'       [15]    [ 78208916]
    'KIRP-BQ-5892-TP'    'RRN3P1'          [16]    [ 21817457]
    'KIRP-BQ-5892-TP'    'MADCAM1'         [19]    [   501762]
    'KIRP-BQ-5892-TP'    'LOC96610'        [22]    [ 22663086]
    'KIRP-BQ-5892-TP'    'LOC100133050'    [ 5]    [ 99715528]
    'KIRP-BQ-5892-TP'    'RPL23AP53'       [ 8]    [   163401]
    'KIRP-BQ-5892-TP'    'TUBBP5'          [ 9]    [141070969]
    'KIRP-BQ-5893-TP'    'LOC642826'       [10]    [ 47207813]
    'KIRP-BQ-5893-TP'    'LRP1'            [12]    [ 57566959]
    'KIRP-BQ-5894-TP'    'RPSAP58'         [19]    [ 24010294]
    'KIRP-BQ-5894-TP'    'RGPD5'           [ 2]    [113127775]
    'KIRP-BQ-5894-TP'    'NUDT11'          [23]    [ 51239296]
    'KIRP-BQ-7044-TP'    'KRTAP4-9'        [17]    [ 39262083]
    'KIRP-BQ-7044-TP'    'PLAC4'           [21]    [ 42551311]
    'KIRP-BQ-7045-TP'    'LOC650368'       [11]    [  3427845]
    'KIRP-BQ-7045-TP'    'DDX11'           [12]    [ 31242861]
    'KIRP-BQ-7045-TP'    'TMEM52'          [ 1]    [  1850628]
    'KIRP-BQ-7045-TP'    'PLAC4'           [21]    [ 42551103]
    'KIRP-BQ-7045-TP'    'HDAC2'           [ 6]    [114292110]
    'KIRP-BQ-7046-TP'    'NBPF1'           [ 1]    [ 16918653]
    'KIRP-BQ-7048-TP'    'RRN3P3'          [16]    [ 22441236]
    'KIRP-BQ-7048-TP'    'FLJ10661'        [ 8]    [  8092055]
    'KIRP-BQ-7048-TP'    'KANK3'           [19]    [  8398950]
    'KIRP-BQ-7049-TP'    'ULBP2'           [ 6]    [150263283]
    'KIRP-BQ-7049-TP'    'ADAM6'           [14]    [106919168]
    'KIRP-BQ-7050-TP'    'HRCT1'           [ 9]    [ 35906559]
    'KIRP-BQ-7050-TP'    'KCNG2'           [18]    [ 77623691]
    'KIRP-BQ-7050-TP'    'MSH3'            [ 5]    [ 79950727]
    'KIRP-BQ-7051-TP'    'POM121L9P'       [22]    [ 24659578]
    'KIRP-BQ-7051-TP'    'POM121L9P'       [22]    [ 24659591]
    'KIRP-BQ-7051-TP'    'POM121L9P'       [22]    [ 24659593]
    'KIRP-BQ-7051-TP'    'CYP21A2'         [ 6]    [ 31974158]
    'KIRP-BQ-7051-TP'    'POLDIP2'         [17]    [ 26684394]
    'KIRP-BQ-7053-TP'    'Unknown'         [10]    [ 48968566]
    'KIRP-BQ-7055-TP'    'LOC650368'       [11]    [  3427845]
    'KIRP-BQ-7056-TP'    'HSD17B7P2'       [10]    [ 38654432]
    'KIRP-BQ-7056-TP'    'ANKRD20B'        [ 2]    [ 95522772]
    'KIRP-BQ-7056-TP'    'C21orf99'        [21]    [ 14439208]
    'KIRP-BQ-7056-TP'    'KRT1'            [12]    [ 53069236]
    'KIRP-BQ-7058-TP'    'RPL23AP32'       [ 2]    [ 54756736]
    'KIRP-BQ-7058-TP'    'ANKRD20B'        [ 2]    [ 95522786]
    'KIRP-BQ-7058-TP'    'MLLT3'           [ 9]    [ 20414346]
    'KIRP-BQ-7058-TP'    'LOC442421'       [ 9]    [ 66499867]
    'KIRP-BQ-7059-TP'    'C21orf99'        [21]    [ 14439357]
    'KIRP-BQ-7059-TP'    'RPL23AP53'       [ 8]    [   163187]
    'KIRP-BQ-7059-TP'    'RPL23AP53'       [ 8]    [   163215]
    'KIRP-BQ-7059-TP'    'TMEM121'         [14]    [105996050]
    'KIRP-BQ-7060-TP'    'FLJ36000'        [17]    [ 21904139]
    'KIRP-BQ-7062-TP'    'LOC284232'       [13]    [ 19415742]
    'KIRP-BQ-7062-TP'    'ST7'             [ 7]    [116869938]
    'KIRP-DW-5560-TP'    'Unknown'         [12]    [ 31307356]
    'KIRP-DW-5560-TP'    'UPF3A'           [13]    [115047559]
    'KIRP-DW-5560-TP'    'TPTE'            [21]    [ 11014987]
    'KIRP-DW-5561-TP'    'FLJ36000'        [17]    [ 21904125]
    'KIRP-DW-5561-TP'    'MLLT3'           [ 9]    [ 20414340]
    'KIRP-DW-5561-TP'    'MAP3K9'          [14]    [ 71275774]
    'KIRP-DW-5561-TP'    'STAG3L2'         [ 7]    [ 74300557]
    'KIRP-DW-5561-TP'    'FOXE1'           [ 9]    [100616701]
    'KIRP-DW-7834-TP'    'NBPF1'           [ 1]    [ 16918653]
    'KIRP-DW-7834-TP'    'ADAM6'           [14]    [107062402]
    'KIRP-DW-7834-TP'    'GOLGA6L10'       [15]    [ 82635117]
    'KIRP-DW-7834-TP'    'CLDN7'           [17]    [  7163815]
    'KIRP-DW-7834-TP'    'PTPN18'          [ 2]    [131129929]
    'KIRP-DW-7834-TP'    'ZNF717'          [ 3]    [ 75790810]
    'KIRP-DW-7837-TP'    'CLDN7'           [17]    [  7163815]
    'KIRP-DW-7837-TP'    'C21orf99'        [21]    [ 14439208]
    'KIRP-DW-7838-TP'    'EPHA2'           [ 1]    [ 16456043]
    'KIRP-DW-7838-TP'    'RAB12'           [18]    [  8609872]
    'KIRP-DW-7838-TP'    'HRCT1'           [ 9]    [ 35906559]
    'KIRP-DW-7838-TP'    'ZXDB'            [23]    [ 57619097]
    'KIRP-DW-7839-TP'    'CROCC'           [ 1]    [ 17272075]
    'KIRP-DW-7839-TP'    'ST7'             [ 7]    [116869938]
    'KIRP-DW-7839-TP'    'OR2T35'          [ 1]    [248801602]
    'KIRP-DW-7840-TP'    'MST1P2'          [ 1]    [ 16974745]
    'KIRP-DW-7840-TP'    'SSPO'            [ 7]    [149518533]
    'KIRP-DW-7841-TP'    'ARRB2'           [17]    [  4623596]
    'KIRP-DW-7841-TP'    'TBP'             [ 6]    [170871058]
    'KIRP-DW-7841-TP'    'ST7'             [ 7]    [116869938]
    'KIRP-DW-7841-TP'    'MICALCL'         [11]    [ 12316384]
    'KIRP-DW-7841-TP'    'ERCC5'           [13]    [103524612]
    'KIRP-DW-7842-TP'    'LOC642826'       [10]    [ 47207813]
    'KIRP-DW-7842-TP'    'ADAMTS7'         [15]    [ 79059041]
    'KIRP-DZ-6131-TP'    'FLJ36000'        [17]    [ 21904069]
    'KIRP-DZ-6131-TP'    'LOC100133050'    [ 5]    [ 99715528]
    'KIRP-DZ-6131-TP'    'Unknown'         [ 1]    [243251423]
    'KIRP-DZ-6132-TP'    'HSD17B7P2'       [10]    [ 38654432]
    'KIRP-DZ-6132-TP'    'ADAM6'           [14]    [107062360]
    'KIRP-DZ-6132-TP'    'EEF1B2'          [ 2]    [207025358]
    'KIRP-DZ-6133-TP'    'HSD17B7P2'       [10]    [ 38654432]
    'KIRP-DZ-6133-TP'    'BCL11B'          [14]    [ 99641544]
    'KIRP-DZ-6134-TP'    'C21orf99'        [21]    [ 14414855]
    'KIRP-DZ-6134-TP'    'UPF3A'           [13]    [115047559]
    'KIRP-DZ-6134-TP'    'CYP2D7P1'        [22]    [ 42538870]
    'KIRP-DZ-6134-TP'    'SLAMF1'          [ 1]    [160589601]
    'KIRP-DZ-6134-TP'    'AGAP4'           [10]    [ 46342668]
    'KIRP-DZ-6134-TP'    'FNBP4'           [11]    [ 47788664]
    'KIRP-DZ-6134-TP'    'AGAP4'           [10]    [ 46342668]
    'KIRP-DZ-6135-TP'    'CROCCL1'         [ 1]    [ 16946434]
    'KIRP-DZ-6135-TP'    'LOC650368'       [11]    [  3427845]
    'KIRP-DZ-6135-TP'    'ADAM6'           [14]    [107062402]
    'KIRP-DZ-6135-TP'    'ADAM6'           [14]    [106919168]
    'KIRP-EV-5902-TP'    'LOC650368'       [11]    [  3427845]
    'KIRP-EV-5902-TP'    'NCOA3'           [20]    [ 46279830]
    'KIRP-EV-5903-TP'    'MUC4'            [ 3]    [195505813]
    'KIRP-EV-5903-TP'    'UGT2B10'         [ 4]    [ 69870669]
    'KIRP-G7-6789-TP'    'HSD17B7P2'       [10]    [ 38654432]
    'KIRP-G7-6789-TP'    'EP400'           [12]    [132547087]
    'KIRP-G7-6789-TP'    'EP400'           [12]    [132547093]
    'KIRP-G7-6789-TP'    'TUBBP5'          [ 9]    [141070969]
    'KIRP-G7-6789-TP'    'TUBBP5'          [ 9]    [141071110]
    'KIRP-G7-6789-TP'    'UBXN11'          [ 1]    [ 26608820]
    'KIRP-G7-6790-TP'    'KRTAP4-11'       [17]    [ 39274087]
    'KIRP-G7-6790-TP'    'MEF2B'           [19]    [ 19258537]
    'KIRP-G7-6792-TP'    'HSD17B7P2'       [10]    [ 38654432]
    'KIRP-G7-6793-TP'    'EP400'           [12]    [132547093]
    'KIRP-G7-6793-TP'    'TMEM121'         [14]    [105996050]
    'KIRP-G7-6795-TP'    'Unknown'         [15]    [102292785]
    'KIRP-G7-6795-TP'    'C9orf86'         [ 9]    [139734633]
    'KIRP-G7-6796-TP'    'Unknown'         [14]    [ 19857036]
    'KIRP-G7-6796-TP'    'KRTAP4-11'       [17]    [ 39274291]
    'KIRP-G7-7501-TP'    'ZNF814'          [19]    [ 58385762]
    'KIRP-G7-7501-TP'    'Unknown'         [ 9]    [ 68413570]
    'KIRP-G7-7501-TP'    'PCSK9'           [ 1]    [ 55505552]
    'KIRP-G7-7502-TP'    'NAB2'            [12]    [ 57485457]
    'KIRP-G7-7502-TP'    'ADAM6'           [14]    [107062402]
    'KIRP-G7-7502-TP'    'POTEC'           [18]    [ 14513764]
    'KIRP-GL-6846-TP'    'UPF3A'           [13]    [115047559]
    'KIRP-GL-6846-TP'    'SYN2'            [ 3]    [ 12046124]
    'KIRP-GL-7773-TP'    'Unknown'         [15]    [102292785]
    'KIRP-GL-7773-TP'    'LOC100133050'    [ 5]    [ 99715528]
    'KIRP-GL-7966-TP'    'PRG4'            [ 1]    [186276100]
    'KIRP-GL-7966-TP'    'FAM86D'          [ 3]    [ 75476630]
    'KIRP-GL-7966-TP'    'CROCCL1'         [ 1]    [ 16946407]
    'KIRP-GL-7966-TP'    'Unknown'         [15]    [102292770]
    'KIRP-GL-7966-TP'    'POM121L9P'       [22]    [ 24659591]
    'KIRP-GL-7966-TP'    'POM121L9P'       [22]    [ 24659593]
    'KIRP-GL-7966-TP'    'FAM86D'          [ 3]    [ 75476630]
    'KIRP-GL-7966-TP'    'MSH3'            [ 5]    [ 79950742]
    'KIRP-HE-7128-TP'    'RP9'             [ 7]    [ 33139017]
    'KIRP-HE-7129-TP'    'Unknown'         [11]    [ 55065601]
    'KIRP-HE-7129-TP'    'ARHGAP11B'       [15]    [ 30938440]
    'KIRP-HE-7129-TP'    'EEF1B2'          [ 2]    [207025358]
    'KIRP-HE-7130-TP'    'LOC653544'       [10]    [135491085]
    'KIRP-HE-7130-TP'    'THSD1P1'         [13]    [ 52864001]
    'KIRP-HE-7130-TP'    'ADAM6'           [14]    [107062360]
    'KIRP-HE-7130-TP'    'HLA-A'           [ 6]    [ 29910693]
    'KIRP-HE-7130-TP'    'RPL23AP53'       [ 8]    [   163187]
    'KIRP-J7-6720-TP'    'ZNF814'          [19]    [ 58385546]
    'KIRP-J7-6720-TP'    'LYPLA2P1'        [ 6]    [ 33333333]
    'KIRP-J7-6720-TP'    'LYPLA2P1'        [ 6]    [ 33333342]

  Column 5

    'C'             
    'A'             
    '-'             
    'C'             
    'C'             
    'G'             
    'A'             
    '-'             
    'A'             
    'G'             
    'C'             
    'A'             
    '-'             
    '-'             
    'A'             
    'T'             
    '-'             
    '-'             
    'C'             
    'T'             
    'T'             
    'T'             
    'CT'            
    '-'             
    'GGT'           
    'G'             
    'G'             
    'C'             
    'A'             
    'A'             
    'C'             
    'C'             
    'T'             
    'A'             
    'G'             
    'T'             
    'T'             
    'A'             
    'A'             
    'AGTAATACACGGCA'
    'G'             
    'A'             
    'T'             
    'C'             
    'C'             
    'C'             
    'G'             
    'C'             
    'T'             
    'T'             
    'T'             
    'G'             
    'C'             
    'C'             
    'GA'            
    'G'             
    'T'             
    'G'             
    'G'             
    'A'             
    'A'             
    '-'             
    'T'             
    'G'             
    'T'             
    'G'             
    'A'             
    'C'             
    'G'             
    'G'             
    'A'             
    'A'             
    'C'             
    'A'             
    'A'             
    '-'             
    'G'             
    'T'             
    'T'             
    'G'             
    'A'             
    'G'             
    'T'             
    'T'             
    'C'             
    'T'             
    'T'             
    'A'             
    'T'             
    'T'             
    'G'             
    'T'             
    'T'             
    '-'             
    '-'             
    'G'             
    '-'             
    '-'             
    'C'             
    'G'             
    'T'             
    'A'             
    'T'             
    'T'             
    'C'             
    'C'             
    'T'             
    'A'             
    'T'             
    'C'             
    'T'             
    'T'             
    '-'             
    'C'             
    'A'             
    'A'             
    'C'             
    '-'             
    '-'             
    '-'             
    'G'             
    'T'             
    'G'             
    'A'             
    'T'             
    'G'             
    'G'             
    'G'             
    'GG'            
    'G'             
    'T'             
    'C'             
    'T'             
    '-'             
    '-'             
    'C'             
    '-'             
    '-'             
    'G'             
    'A'             
    'T'             
    'CA'            
    'G'             
    'A'             
    'G'             
    '-'             
    'T'             
    'C'             
    'A'             
    'G'             
    'G'             
    '-'             
    '-'             
    'G'             
    'G'             
    'C'             
    'T'             
    '-'             
    'T'             
    'A'             
    'G'             
    'T'             
    '-'             
    'C'             
    '-'             
    'C'             
    '-'             
    'C'             
    'G'             
    'A'             
    'C'             
    'G'             
    'T'             
    'C'             
    'G'             
    'C'             
    'A'             
    'G'             
    'C'             
    '-'             
    'C'             
    'G'             
    'T'             
    'C'             
    '-'             
    'C'             
    '-'             
    'T'             
    'A'             
    'A'             
    '-'             
    'G'             
    '-'             
    'C'             
    'GGC'           
    'CAGCGCCCC'     
    'G'             
    'G'             
    'T'             
    'G'             
    'G'             
    'G'             
    'T'             
    'G'             
    'C'             
    'G'             
    '-'             
    'CC'            
    'C'             
    'A'             
    'C'             
    'G'             
    'C'             
    'A'             
    '-'             
    'G'             
    'C'             
    'C'             
    'C'             
    'T'             
    'G'             
    'A'             
    'A'             
    '-'             
    '-'             
    '-'             
    'T'             
    'C'             
    'C'             
    'C'             
    '-'             
    'T'             
    'C'             
    'G'             
    'C'             
    'A'             
    'C'             
    'A'             
    'A'             
    'C'             
    'CA'            
    'A'             
    '-'             
    'G'             
    'A'             
    'C'             
    '-'             
    '-'             
    'C'             
    'C'             
    'G'             
    'T'             
    '-'             
    'G'             
    'G'             
    'G'             
    'G'             
    '-'             
    'G'             
    'T'             
    'C'             
    '-'             
    '-'             
    '-'             
    '-'             
    'T'             
    'T'             
    'C'             
    '-'             
    'T'             
    'A'             
    'C'             
    'A'             
    'G'             
    'A'             
    'G'             
    'G'             
    'G'             
    '-'             
    'C'             
    'C'             
    'G'             
    'G'             
    '-'             
    'G'             
    '-'             
    'G'             
    'C'             
    'G'             
    'A'             
    'CTG'           
    'C'             
    'C'             
    'T'             
    'T'             
    '-'             
    'G'             
    'T'             
    'C'             
    'G'             
    'G'             
    'T'             
    'G'             
    'T'             
    'G'             
    '-'             
    'C'             
    'G'             
    'G'             
    'G'             
    'A'             
    'G'             
    'G'             
    'G'             
    'C'             
    'T'             
    'A'             
    'A'             

Removing the following non-coding mutations (based on "type" field):
          RNA: [225]
    ----TOTAL: [225]
Not enforcing any target list.
Collapsing adjacent mutations:
convert_chr: assuming human for chrX/chrY

    2 SNPs to one Complex_substitution (guessing "Missense"): [1]
                     2 SNPs to one DNP (guessing "Missense"): [20]
                                    2 SNPs/Indels to one SNP: [44]
                                 2 redundant SNPs to one SNP: [437]
                                 3 redundant SNPs to one SNP: [1]
                     4 SNPs to one DNP (guessing "Missense"): [1]
                                    4 SNPs/Indels to one SNP: [13]
                                 4 redundant SNPs to one SNP: [214]
    6 SNPs to one Complex_substitution (guessing "Missense"): [1]
                                                   ----TOTAL: [732]

Genes affected:
            ABCA4: [1]
            ABCB6: [1]
            ABCE1: [1]
            ABCG4: [1]
             ABRA: [1]
            ACAP2: [1]
              ACE: [1]
            ACTA1: [1]
            ACTG2: [1]
           ADAM12: [1]
         ADAMTS14: [1]
         ADAMTS17: [1]
         ADAMTS19: [1]
         ADAMTSL3: [1]
            ADCY3: [1]
             AFF3: [1]
            AGGF1: [1]
              AGL: [1]
              AGT: [1]
          AGXT2L2: [1]
            AJAP1: [1]
             ALAD: [1]
          ALDH1B1: [1]
            AMY2B: [1]
           ANAPC5: [1]
           ANGEL1: [1]
           ANGPT2: [1]
           ANKFY1: [1]
            ANKK1: [1]
          ANKRD44: [1]
            ANXA3: [1]
            AP4M1: [1]
            APBA2: [1]
            APBA3: [1]
            APLNR: [1]
             APTX: [1]
             ARF5: [1]
          ARFGEF2: [1]
         ARHGAP24: [1]
         ARHGEF37: [1]
           ARID1B: [1]
            ARRB1: [1]
            ASB15: [1]
             ASB4: [1]
            ASGR1: [1]
            ASH1L: [1]
             ATF7: [1]
          ATP13A3: [1]
           ATP2B3: [1]
          ATP6V1A: [1]
           ATRNL1: [1]
             ATRX: [1]
           BAT2L2: [1]
             BCAN: [1]
           BCKDHA: [1]
           BEGAIN: [1]
             BHMT: [1]
             BIN3: [1]
             BMP1: [1]
            BMP15: [1]
           BMPR1B: [1]
             BNC2: [1]
             BRAF: [1]
            BSDC1: [1]
           BTBD12: [1]
            BTBD6: [1]
             BTG2: [1]
         C10orf12: [1]
         C11orf80: [1]
         C12orf41: [1]
         C15orf52: [1]
          C16orf7: [1]
         C16orf86: [1]
         C19orf21: [1]
         C19orf50: [1]
          C1orf55: [1]
          C1orf66: [1]
         C20orf12: [1]
        C20orf141: [1]
           C2orf3: [1]
          C7orf26: [1]
          C9orf24: [1]
            CABC1: [1]
           CABIN1: [1]
          CACNA1B: [1]
           CACNG2: [1]
           CACNG4: [1]
           CALML4: [1]
           CAMK1D: [1]
           CAMKK1: [1]
            CAPN5: [1]
            CASC3: [1]
          CCDC108: [1]
          CCDC132: [1]
           CCDC63: [1]
           CCDC78: [1]
            CCKAR: [1]
            CD209: [1]
             CD40: [1]
            CDC5L: [1]
            CDK13: [1]
           CDK5R1: [1]
            CDKL2: [1]
              CEL: [1]
           CELSR1: [1]
           CEP350: [1]
             CERK: [1]
             CHD1: [1]
             CHD4: [1]
             CHD7: [1]
            CHRM2: [1]
           CHRNB3: [1]
            CHRND: [1]
           CLINT1: [1]
            CLOCK: [1]
           CLSTN1: [1]
            CNGB1: [1]
           CNOT10: [1]
          COL17A1: [1]
          COL22A1: [1]
           COL4A3: [1]
           CORO1B: [1]
            CPEB3: [1]
            CPNE7: [1]
            CPXM1: [1]
            CRIP3: [1]
             CRNN: [1]
           CTAGE1: [1]
            CTCFL: [1]
            CTPS2: [1]
            CWH43: [1]
           CX3CL1: [1]
            CYHR1: [1]
           CYP2S1: [1]
            CYTSB: [1]
           DAZAP1: [1]
            DBF4B: [1]
             DBN1: [1]
            DCTN1: [1]
             DDR1: [1]
           DEPDC5: [1]
            DIRC2: [1]
             DLG1: [1]
            DMXL2: [1]
            DOCK1: [1]
            DOCK5: [1]
           DPAGT1: [1]
             DRD3: [1]
             DSC2: [1]
              DST: [1]
          DULLARD: [1]
          DYNC1H1: [1]
          DYNC1I1: [1]
             EEF2: [1]
             EFHB: [1]
            EGLN2: [1]
          EIF2AK3: [1]
            EIF3G: [1]
             ELF3: [1]
            ELTD1: [1]
            ENPP7: [1]
            EP300: [1]
            EP400: [1]
          EPB41L1: [1]
            EPB42: [1]
            EPHA8: [1]
           ERLIN2: [1]
            ESPNP: [1]
            ETAA1: [1]
             EVI5: [1]
           EXOSC9: [1]
              EYS: [1]
               F5: [1]
           FABP12: [1]
          FAM123B: [1]
          FAM135A: [1]
          FAM188A: [1]
           FAM20A: [1]
           FAM60A: [1]
          FAM71F1: [1]
           FAM83G: [1]
           FAM86A: [1]
             FAT1: [1]
             FBN3: [1]
           FBXO11: [1]
           FBXW12: [1]
             FGD5: [1]
            FGF21: [1]
            FGFR4: [1]
             FGGY: [1]
               FH: [1]
            FKBP3: [1]
              FLG: [1]
             FLNB: [1]
             FLT4: [1]
            FREM1: [1]
            FRMD6: [1]
             FRYL: [1]
             FSCB: [1]
             FZD1: [1]
             FZD5: [1]
           GABRB3: [1]
           GABRG2: [1]
             GCH1: [1]
            GFPT2: [1]
             GGA2: [1]
             GIPR: [1]
           GLB1L2: [1]
             GLDN: [1]
             GLI1: [1]
             GNAZ: [1]
           GOLGB1: [1]
           GOLT1A: [1]
            GP1BA: [1]
             GPC4: [1]
            GPNMB: [1]
            GPR45: [1]
            GPR55: [1]
            GRHL1: [1]
            GRHL2: [1]
             GRM4: [1]
             GSG1: [1]
            GSTT1: [1]
           GTF3C2: [1]
           GTF3C5: [1]
            GTSE1: [1]
             GYG2: [1]
             GYS2: [1]
           HARBI1: [1]
          HCFC1R1: [1]
            HDHD2: [1]
            HECW1: [1]
             HELQ: [1]
         HLA-DQA2: [1]
           HMG20A: [1]
            HNF4A: [1]
             HNMT: [1]
              HPX: [1]
            HSDL2: [1]
           HSPA1L: [1]
            HYDIN: [1]
            ICA1L: [1]
              IDE: [1]
            IFIH1: [1]
           IFT140: [1]
           IGDCC3: [1]
            IL4I1: [1]
             IL4R: [1]
             IL9R: [1]
             IMMT: [1]
            INSM2: [1]
            INSRR: [1]
            INTS2: [1]
            ITGAE: [1]
            ITGB5: [1]
            ITGB7: [1]
           ITPRIP: [1]
             JAG2: [1]
           KBTBD6: [1]
            KCNH1: [1]
            KCNH7: [1]
           KCNK13: [1]
            KCNN1: [1]
           KCTD11: [1]
           KCTD20: [1]
            KDM4A: [1]
         KIAA0226: [1]
         KIAA0467: [1]
         KIAA0528: [1]
         KIAA0664: [1]
         KIAA0753: [1]
         KIAA0907: [1]
         KIAA1407: [1]
         KIAA1429: [1]
         KIAA1598: [1]
         KIAA1826: [1]
         KIAA1984: [1]
            KLHL1: [1]
           KLHL35: [1]
            KNDC1: [1]
             KPTN: [1]
            KRBA1: [1]
            KRT13: [1]
            KRT83: [1]
        KRTAP10-3: [1]
            LAMB1: [1]
            LASS2: [1]
            LCE3D: [1]
            LCN12: [1]
            LENG8: [1]
           LEPRE1: [1]
             LGI4: [1]
           LHFPL4: [1]
           LILRA3: [1]
           LILRB4: [1]
             LMLN: [1]
             LNX2: [1]
         LOC81691: [1]
            LRCH1: [1]
            LRIG1: [1]
             LRP2: [1]
           LRRC33: [1]
            LRRN2: [1]
              LSS: [1]
            MACC1: [1]
            MANBA: [1]
          MAP3K14: [1]
           MAP4K4: [1]
           MAPK15: [1]
            MARS2: [1]
               MB: [1]
           MCOLN3: [1]
            MCTP2: [1]
            MDGA2: [1]
              MET: [1]
             MGAM: [1]
             MKKS: [1]
             MKL1: [1]
             MLH3: [1]
             MLL3: [1]
            MLLT4: [1]
              MLX: [1]
            MMP24: [1]
              MNT: [1]
            MOSC1: [1]
              MPO: [1]
          MRGPRX1: [1]
           MRPL13: [1]
             MRS2: [1]
           MS4A15: [1]
            MUC16: [1]
            MXRA5: [1]
           MYBPC2: [1]
            MYH13: [1]
             MYH2: [1]
             MYH7: [1]
            MYO1H: [1]
            MYO5B: [1]
            MYO5C: [1]
            MYO9A: [1]
            NALCN: [1]
           NBEAL2: [1]
           NBPF14: [1]
            NCOR1: [1]
            NCOR2: [1]
             NEBL: [1]
             NEO1: [1]
              NF2: [1]
           NFE2L3: [1]
            NICN1: [1]
             NINL: [1]
            NKPD1: [1]
            NLRP9: [1]
             NME5: [1]
           NPEPL1: [1]
          NR2C2AP: [1]
            NRCAM: [1]
            NRIP1: [1]
             NSD1: [1]
          NSUN5P1: [1]
             NTN3: [1]
            NUAK2: [1]
            NXNL1: [1]
            OBSCN: [1]
            OBSL1: [1]
             ODF4: [1]
             OGG1: [1]
           OR14J1: [1]
            OR1D4: [1]
            OR2Y1: [1]
           OR4C11: [1]
            OR4S2: [1]
           OR56A1: [1]
            OR6Y1: [1]
             PAOX: [1]
           PAPOLG: [1]
            PAPPA: [1]
            PARP3: [1]
            PARVB: [1]
           PCDH12: [1]
           PCDH18: [1]
           PCDH20: [1]
          PCDHB10: [1]
         PCDHGA12: [1]
          PCDHGA2: [1]
          PCDHGA3: [1]
          PCDHGB7: [1]
            PCF11: [1]
            PCIF1: [1]
           PCNXL2: [1]
            PCSK1: [1]
           PCYT1A: [1]
           PDE11A: [1]
            PDIA6: [1]
           PDXDC1: [1]
             PEX5: [1]
             PFAS: [1]
           PGGT1B: [1]
            PHKA1: [1]
            PICK1: [1]
           PIK3R2: [1]
          PIP5K1C: [1]
            PIPOX: [1]
           PKDREJ: [1]
            PLCB2: [1]
          PLEKHA6: [1]
          PLEKHG1: [1]
          PLEKHG5: [1]
            PLRG1: [1]
           PLXDC2: [1]
             POGZ: [1]
          POLDIP2: [1]
             POLQ: [1]
           POLR2A: [1]
            POSTN: [1]
          PPP2R5C: [1]
            PPRC1: [1]
          PRAMEF1: [1]
             PREP: [1]
           PRKAG2: [1]
            PROM1: [1]
            PROSC: [1]
          PRPF40A: [1]
            PRR12: [1]
           PRSS16: [1]
           PRSS21: [1]
            PSMB4: [1]
            PSMC4: [1]
            PSMD8: [1]
            PTCD1: [1]
            PTCH1: [1]
           PTPN18: [1]
           PTPN22: [1]
            PTPRE: [1]
             PUM2: [1]
             PUS3: [1]
          PYROXD2: [1]
           QRICH2: [1]
           RAB27B: [1]
          RABGAP1: [1]
          RAD54L2: [1]
           RAET1L: [1]
             RAF1: [1]
         RAP1GAP2: [1]
          RAPGEF3: [1]
            RBBP6: [1]
            RDH12: [1]
             RDM1: [1]
             RELN: [1]
            REV3L: [1]
             RFX2: [1]
           RHBDL3: [1]
            RHPN1: [1]
            RIC8A: [1]
            RIMS1: [1]
            RIPK2: [1]
             ROS1: [1]
           RPL37A: [1]
             RRN3: [1]
            RRP12: [1]
           RSPH6A: [1]
            RUFY3: [1]
            SAPS3: [1]
           SCARF1: [1]
           SCN10A: [1]
            SCN8A: [1]
           SCUBE3: [1]
             SDF4: [1]
           SEC23A: [1]
          SEC23IP: [1]
            SEC62: [1]
             SELE: [1]
           SEMA5A: [1]
        SERPINB10: [1]
         SERPINE1: [1]
           SESTD1: [1]
            SETD4: [1]
           SEZ6L2: [1]
           SFMBT1: [1]
            SGMS1: [1]
           SH3RF3: [1]
           SHANK1: [1]
              SHE: [1]
          SHROOM1: [1]
            SIDT2: [1]
          SIGLEC9: [1]
          SLC13A2: [1]
          SLC16A5: [1]
           SLC1A1: [1]
          SLC22A2: [1]
          SLC24A3: [1]
          SLC25A1: [1]
          SLC26A9: [1]
         SLC38A10: [1]
          SLC39A5: [1]
          SLC43A1: [1]
          SLC43A3: [1]
          SLC5A12: [1]
           SLC5A3: [1]
          SLC6A11: [1]
          SLC6A18: [1]
           SLC6A9: [1]
          SLCO2A1: [1]
              SLK: [1]
          SMARCB1: [1]
          SMARCC2: [1]
             SMG1: [1]
            SMPD2: [1]
            SNRPN: [1]
            SNTB1: [1]
            SNX29: [1]
            SOX10: [1]
            SP110: [1]
            SPAG5: [1]
          SPATA17: [1]
           SPRED2: [1]
           SPTAN1: [1]
           SRCIN1: [1]
            SRRM1: [1]
            SRRM2: [1]
            SRRM4: [1]
             SSR3: [1]
             ST7L: [1]
            STAG2: [1]
          STARD10: [1]
           STARD3: [1]
            STAT1: [1]
    STON1-GTF2A1L: [1]
          STXBP5L: [1]
          SULT1C4: [1]
            SUSD2: [1]
            SYNE1: [1]
             SYNM: [1]
              SYP: [1]
             SYT4: [1]
            TAF1B: [1]
           TAS1R3: [1]
           TAS2R1: [1]
             TBCD: [1]
             TBCK: [1]
            TCFL5: [1]
             TDP1: [1]
           TDRD10: [1]
             TET2: [1]
             TEX2: [1]
            TFCP2: [1]
             TGFA: [1]
            TGIF1: [1]
            THBS1: [1]
           THRAP3: [1]
            TIGD2: [1]
             TMC3: [1]
            TMCC2: [1]
            TMCO7: [1]
         TMEM120A: [1]
         TMEM167A: [1]
            TMEM2: [1]
         TMEM200B: [1]
           TMEM37: [1]
           TMEM79: [1]
             TMPO: [1]
           TNFSF8: [1]
            TNKS2: [1]
            TOP2B: [1]
            TOR1A: [1]
             TP53: [1]
          TP53TG5: [1]
            TPPP3: [1]
           TRIM28: [1]
           TRIML1: [1]
             TRIO: [1]
            TRPC3: [1]
            TRPV2: [1]
             TRY6: [1]
             TSC2: [1]
             TSFM: [1]
         TSNAXIP1: [1]
            TTC25: [1]
            TTLL1: [1]
           TUBA4A: [1]
           TXNRD1: [1]
            TYRO3: [1]
            TYRP1: [1]
             UACA: [1]
              UBC: [1]
            UBE3A: [1]
             UBR4: [1]
           UGT2A3: [1]
           UGT2B7: [1]
            ULBP1: [1]
             ULK1: [1]
           UNC13D: [1]
            UNC50: [1]
            UNC5C: [1]
             UPP2: [1]
             USF1: [1]
            USH2A: [1]
            USP28: [1]
            USP34: [1]
            USP35: [1]
             VARS: [1]
            VARS2: [1]
              VCP: [1]
            VLDLR: [1]
           VPS13C: [1]
            VPS4B: [1]
             VRK3: [1]
            VWC2L: [1]
             VWCE: [1]
          WBSCR17: [1]
            WDR11: [1]
            WDR41: [1]
            WDR54: [1]
            WDR55: [1]
            WDR59: [1]
            WDR66: [1]
           WNT10A: [1]
             WTAP: [1]
            XIRP2: [1]
             XPR1: [1]
           ZBTB11: [1]
           ZBTB46: [1]
           ZBTB49: [1]
           ZCWPW1: [1]
           ZDHHC7: [1]
             ZEB1: [1]
          ZFP36L1: [1]
            ZFP41: [1]
            ZMYM3: [1]
          ZMYND11: [1]
           ZNF142: [1]
           ZNF180: [1]
            ZNF20: [1]
           ZNF214: [1]
           ZNF226: [1]
           ZNF232: [1]
          ZNF324B: [1]
           ZNF439: [1]
           ZNF546: [1]
           ZNF568: [1]
           ZNF615: [1]
           ZNF627: [1]
           ZNF700: [1]
           ZNF707: [1]
           ZNF799: [1]
            ZNF99: [1]
            ZNFX1: [1]
          ZSCAN18: [1]
           ZSWIM4: [1]
            ZZEF1: [1]
             ACTB: [2]
           ATP1A1: [2]
              B2M: [2]
             BRD2: [2]
            CCNL2: [2]
           COL6A6: [2]
             DHDH: [2]
            DIP2C: [2]
            DNAH9: [2]
            EPHB6: [2]
             EPN3: [2]
         FLJ46321: [2]
           GIGYF2: [2]
             GRM2: [2]
           GTF2H4: [2]
          HSP90B1: [2]
             IPO8: [2]
            LMTK3: [2]
        LOC200030: [2]
            LRIG2: [2]
           LRRC49: [2]
            MACF1: [2]
             MLL2: [2]
            MUC17: [2]
            NCAPH: [2]
              NEB: [2]
            PTPRD: [2]
            SCN2A: [2]
          SIPA1L1: [2]
          SLC26A5: [2]
          SPATA20: [2]
            SRCAP: [2]
             ST18: [2]
           TOPORS: [2]
          Unknown: [2]
              ZAN: [2]
            FGFR3: [3]
              TTN: [3]
          CTTNBP2: [4]
        ----TOTAL: [732]

Patients affected:
    KIRP-B9-4113-TP: [1]
    KIRP-EV-5903-TP: [1]
    KIRP-DZ-6135-TP: [36]
    KIRP-GL-7966-TP: [49]
    KIRP-DZ-6134-TP: [52]
    KIRP-A4-7732-TP: [63]
    KIRP-GL-6846-TP: [79]
    KIRP-B3-4103-TP: [87]
    KIRP-B3-3925-TP: [95]
    KIRP-DZ-6133-TP: [126]
    KIRP-B3-4104-TP: [143]
          ----TOTAL: [732]
convert_chr: assuming human for chrX/chrY
Collapsed 8472 muts to 7279 muts
Getting context: 
Done.
Saved KIRP-TP.mutation_preprocessing_report.txt
Saved KIRP-TP.maf
Total of 100 patients had both MAF and WIG data.
Saved KIRP-TP.patients.txt
Saved KIRP-TP.coverage.prepare.txt
libdir: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.90.3705/
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/285884
mFile: fh_MutSigPreprocess
executing: /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.90.3705/fh_MutSigPreprocess /xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/MutSigPreprocess.90.3705/ -i KIRP-TP -b hg19 -t /xchip/cga1/annotation/db/capture/Refseq_exons_good_20101221_hg19.txt -c /xchip/cga1/annotation/db/tracks/hg19/c65e -bd /xchip/cga1/annotation/db/ucsc/hg19 -cat 4 -maf1 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/KIRP-TP/2283891/maf1.input.tsv -maflabel1 Broad -maflabel2 WashU -maflabel3 Baylor -wig1 /xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigPreprocess/KIRP-TP/2283891/wig1.input.tsv -p /xchip/cga1/reference/mutsig_params/MutSig2.0_cga.pancan.blacklist.v7.hg19.params.txt
