├── .gitignore ├── .gitmodules ├── A_Reference ├── BPS_Stage.config ├── README.md └── dat │ ├── GRCh37_selectVirus_9a.bed │ └── GRCh37_selectVirus_9a.fa.fai ├── B_ExonGene ├── 1_get_GTF.sh ├── 2_get_merged_exon_bed.sh ├── 3_get_gene_bed.sh ├── 4_make_virus_names.sh ├── BPS_Stage.config ├── README.md ├── dat │ ├── GRCh38_ensembl2gencode.txt │ ├── Homo_sapiens.GRCh37.75.gtf.gz │ ├── RAD51B.37.75.gtf │ ├── RAD51B.37.75.gtf.tsv │ ├── RAD51B.38.84.gtf │ ├── RAD51B.38.84.gtf.tsv │ ├── exons.ens75.bed │ ├── exons.ens84.bed │ ├── exons.ens84.norm.bed │ ├── genes.ens75.bed │ ├── genes.ens84.bed │ ├── genes.ens84.norm.bed │ └── virus_names.dat ├── x.5_examine_GTF.sh ├── x.6_get_FAI.sh ├── x.7_get_chrom_names.sh └── x.8_normalize_chrom.sh ├── C_Project ├── 1_get_BAM_paths.sh ├── 2_make_RNASeq_paths.sh ├── BPS_Stage.config ├── README.md └── dat │ ├── BPS.expression.samples.dat │ └── BPS.samples.dat ├── Development.md ├── F_PindelRP ├── 1_make_config.sh ├── 2_run_Pindel.sh ├── 3_process_Pindel_RP.sh ├── BPS_Stage.config ├── README.md └── dat │ ├── BPR │ └── TCGA-BA-4077-01B-01D-2268-08.PindelRP.BPR.dat │ ├── TCGA-BA-4077-01B-01D-2268-08_BP │ ├── TCGA-BA-4077-01B-01D-2268-08_CloseEndMapped │ ├── TCGA-BA-4077-01B-01D-2268-08_D │ ├── TCGA-BA-4077-01B-01D-2268-08_INT │ ├── TCGA-BA-4077-01B-01D-2268-08_INT_final │ ├── TCGA-BA-4077-01B-01D-2268-08_INV │ ├── TCGA-BA-4077-01B-01D-2268-08_LI │ ├── TCGA-BA-4077-01B-01D-2268-08_RP │ ├── TCGA-BA-4077-01B-01D-2268-08_SI │ ├── TCGA-BA-4077-01B-01D-2268-08_TD │ └── config │ └── TCGA-BA-4077-01B-01D-2268-08.cfg ├── G_Discordant ├── 1_get_Discordant_reads.sh ├── 2_process_Discordant.sh ├── BPS_Stage.config ├── README.md └── dat │ └── BPC │ └── TCGA-BA-4077-01B-01D-2268-08.Discordant.BPC.dat ├── H_NovoBreak ├── 1_make_synthetic_normal.sh ├── 2_align_synthetic_reads.sh ├── 3_make_ROI_BAM.sh ├── 4_merge_ROI_BAM.sh ├── 5_run_Novobreak.sh ├── 6_make_Novobreak_BPC.sh ├── BPS_Stage.config ├── README.md ├── dat │ ├── BA-4077.ROI.bed │ └── novobreak │ │ └── TCGA-BA-4077-01B-01D-2268-08 │ │ ├── novoBreak.bpc.dat │ │ └── novoBreak.pass.flt.vcf └── src │ └── run_novoBreak.sh ├── INSTALL.md ├── I_Contig ├── 1_make_CTX.sh ├── 2_run_tigra.sh ├── 3_realign.sh ├── 4_rename_contigs.sh ├── 5_make_pSBP.sh ├── 6_make_SBP.sh ├── 7_make_BPC.sh ├── BPS_Stage.config ├── README.md └── dat │ ├── BPC │ ├── TCGA-BA-4077-01B-01D-2268-08.BPC.dat │ └── TCGA-BA-4077-01B-01D-2268-08.qSBP.dat │ ├── BWA │ └── TCGA-BA-4077-01B-01D-2268-08.sam │ ├── CTX │ └── TCGA-BA-4077-01B-01D-2268-08.ctx │ ├── SAM │ └── TCGA-BA-4077-01B-01D-2268-08.QMD5.sam │ ├── SBP │ └── TCGA-BA-4077-01B-01D-2268-08.SBP.dat │ ├── contig │ └── TCGA-BA-4077-01B-01D-2268-08.contig │ └── pSBP │ └── TCGA-BA-4077-01B-01D-2268-08.pSBP.dat ├── J_PlotList ├── 1_make_PindelRP_clusters.sh ├── 2_prioritize_PindelRP.sh ├── 3_make_PlotList.sh ├── BPS_Stage.config ├── README.md └── dat │ ├── BPC │ ├── TCGA-BA-4077-01B-01D-2268-08.Discordant-cluster.BPR.dat │ └── TCGA-BA-4077-01B-01D-2268-08.Discordant-prioritized.BPR.dat │ ├── BPR │ ├── TCGA-BA-4077-01B-01D-2268-08.PindelRP-cluster.BPR.dat │ └── TCGA-BA-4077-01B-01D-2268-08.PindelRP-prioritized.BPR.dat │ └── PlotList.dat ├── K_ReadDepth ├── 1_getReadDepth.sh ├── 2_makeFlagstat.sh ├── 3_makeReadCoverage.sh ├── 4_makeFlagstat.RNA-Seq.sh ├── 5_makeReadCoverage.RNA-Seq.sh ├── BPS_Stage.config ├── README.md └── dat │ ├── RNA-Seq.flagstat.dat │ ├── TCGA-BA-4077-01B-01D-2268-08 │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.A.DEPTH.dat │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.DEPTH.dat │ ├── flagstat.dat │ └── flagstat │ └── TCGA-BA-4077-01B-01D-2268-08.flagstat ├── LICENSE ├── L_Expression ├── 1_make_flanking_BED.sh ├── 2_makeUnifiedBED.sh ├── 3_streamExons.sh ├── 4_get_RPKM.sh ├── 5_create_rpkm_master_datafile.sh ├── 6_evaluate_expression_Pvalue.sh ├── AlgorithmDetails.md ├── BPS_Stage.config ├── README.md └── dat │ ├── BED │ ├── HNSC.roi.bed │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.A.1M.bed │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.1M.bed │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.bed │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.neighbor.exon.bed │ ├── FDR │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.gene.pval.FDR.dat │ ├── HNSC_RPKM.dat │ ├── HNSC_barcodes.dat │ ├── NeighborSummary.dat │ └── RPKM │ ├── TCGA-BA-4074-01A-01R-1436-07.rpkm │ ├── TCGA-BA-4075-01A-01R-1436-07.rpkm │ ├── TCGA-BA-4076-01A-01R-1436-07.rpkm │ ├── TCGA-BA-4077-01B-01R-1436-07.rpkm │ ├── TCGA-BA-4078-01A-01R-1436-07.rpkm │ ├── TCGA-BA-5149-01A-01R-1514-07.rpkm │ ├── TCGA-BA-5151-01A-01R-1436-07.rpkm │ ├── TCGA-BA-5152-01A-02R-1873-07.rpkm │ ├── TCGA-BA-5153-01A-01R-1436-07.rpkm │ ├── TCGA-BA-5555-01A-01R-1514-07.rpkm │ ├── TCGA-BA-5556-01A-01R-1514-07.rpkm │ ├── TCGA-BA-5558-01A-01R-1514-07.rpkm │ ├── TCGA-BA-5559-01A-01R-1514-07.rpkm │ ├── TCGA-BA-6869-01A-11R-1873-07.rpkm │ ├── TCGA-BA-6870-01A-11R-1873-07.rpkm │ ├── TCGA-BA-6871-01A-11R-1873-07.rpkm │ ├── TCGA-BA-6872-01A-11R-1873-07.rpkm │ ├── TCGA-BA-6873-01A-11R-1873-07.rpkm │ ├── TCGA-BA-7269-01A-11R-2016-07.rpkm │ ├── TCGA-BA-A4IF-01A-11R-A266-07.rpkm │ ├── TCGA-BA-A4IG-01A-11R-A266-07.rpkm │ ├── TCGA-BA-A4IH-01A-11R-A266-07.rpkm │ ├── TCGA-BA-A4II-01A-11R-A266-07.rpkm │ ├── TCGA-BA-A6D8-01A-31R-A31N-07.rpkm │ ├── TCGA-BA-A6DA-01A-31R-A31N-07.rpkm │ ├── TCGA-BA-A6DB-01A-11R-A30B-07.rpkm │ ├── TCGA-BA-A6DD-01A-12R-A31N-07.rpkm │ ├── TCGA-BA-A6DE-01A-22R-A31N-07.rpkm │ ├── TCGA-BA-A6DG-01A-21R-A30B-07.rpkm │ ├── TCGA-BA-A6DI-01A-11R-A30B-07.rpkm │ ├── TCGA-BA-A6DJ-01A-11R-A30B-07.rpkm │ ├── TCGA-BA-A6DL-01A-21R-A30B-07.rpkm │ ├── TCGA-BB-4217-01A-11R-2081-07.rpkm │ ├── TCGA-BB-4223-01A-01R-1436-07.rpkm │ ├── TCGA-BB-4224-01A-01R-1436-07.rpkm │ ├── TCGA-BB-4225-01A-01R-1436-07.rpkm │ ├── TCGA-BB-4228-01A-01R-1436-07.rpkm │ ├── TCGA-BB-7861-01A-11R-2232-07.rpkm │ ├── TCGA-BB-7862-01A-21R-2232-07.rpkm │ ├── TCGA-BB-7863-01A-11R-2232-07.rpkm │ ├── TCGA-BB-7866-01A-11R-2232-07.rpkm │ ├── TCGA-BB-7870-01A-11R-2232-07.rpkm │ ├── TCGA-BB-7871-01A-11R-2232-07.rpkm │ ├── TCGA-BB-8596-01A-11R-2403-07.rpkm │ ├── TCGA-BB-8601-01A-11R-2403-07.rpkm │ ├── TCGA-BB-A5HU-01A-11R-A28V-07.rpkm │ ├── TCGA-BB-A5HY-01A-11R-A28V-07.rpkm │ ├── TCGA-BB-A5HZ-01A-21R-A28V-07.rpkm │ ├── TCGA-BB-A6UM-01A-12R-A34R-07.rpkm │ ├── TCGA-BB-A6UO-01A-12R-A34R-07.rpkm │ ├── TCGA-C9-A47Z-01A-11R-A24H-07.rpkm │ ├── TCGA-C9-A480-01A-12R-A24H-07.rpkm │ ├── TCGA-CN-4723-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4725-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4726-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4727-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4728-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4729-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4730-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4731-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4733-01A-02R-1873-07.rpkm │ ├── TCGA-CN-4734-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4735-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4736-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4737-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4738-01A-02R-1514-07.rpkm │ ├── TCGA-CN-4739-01A-02R-1514-07.rpkm │ ├── TCGA-CN-4741-01A-01R-1436-07.rpkm │ ├── TCGA-CN-4742-01A-02R-1514-07.rpkm │ ├── TCGA-CN-5355-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5356-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5358-01A-01R-1514-07.rpkm │ ├── TCGA-CN-5359-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5360-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5361-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5363-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5364-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5365-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5366-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5369-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5370-01A-01R-2016-07.rpkm │ ├── TCGA-CN-5373-01A-01R-1436-07.rpkm │ ├── TCGA-CN-5374-01A-01R-1436-07.rpkm │ ├── TCGA-CN-6010-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6011-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6012-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6013-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6016-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6017-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6018-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6019-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6020-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6021-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6022-01A-21R-1686-07.rpkm │ ├── TCGA-CN-6023-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6024-01A-11R-1686-07.rpkm │ ├── TCGA-CN-6988-01A-11R-1915-07.rpkm │ ├── TCGA-CN-6989-01A-11R-1915-07.rpkm │ ├── TCGA-CN-6992-01A-11R-1915-07.rpkm │ ├── TCGA-CN-6994-01A-11R-1915-07.rpkm │ ├── TCGA-CN-6995-01A-31R-2016-07.rpkm │ ├── TCGA-CN-6996-01A-11R-1915-07.rpkm │ ├── TCGA-CN-6997-01A-11R-2016-07.rpkm │ ├── TCGA-CN-6998-01A-23R-2016-07.rpkm │ ├── TCGA-CN-A497-01A-11R-A24H-07.rpkm │ ├── TCGA-CN-A498-01A-11R-A24H-07.rpkm │ ├── TCGA-CN-A499-01A-11R-A24H-07.rpkm │ ├── TCGA-CN-A49A-01A-11R-A24H-07.rpkm │ ├── TCGA-CN-A49B-01A-31R-A24H-07.rpkm │ ├── TCGA-CN-A49C-01A-11R-A24H-07.rpkm │ ├── TCGA-CN-A63T-01A-11R-A28V-07.rpkm │ ├── TCGA-CN-A63U-01A-11R-A30B-07.rpkm │ ├── TCGA-CN-A63W-01A-11R-A30B-07.rpkm │ ├── TCGA-CN-A641-01A-11R-A30B-07.rpkm │ ├── TCGA-CN-A642-01A-12R-A30B-07.rpkm │ ├── TCGA-CN-A6UY-01A-12R-A34R-07.rpkm │ ├── TCGA-CN-A6V1-01A-12R-A34R-07.rpkm │ ├── TCGA-CN-A6V3-01A-12R-A34R-07.rpkm │ ├── TCGA-CN-A6V6-01A-12R-A34R-07.rpkm │ ├── TCGA-CN-A6V7-01A-12R-A34R-07.rpkm │ ├── TCGA-CQ-5323-01A-01R-1686-07.rpkm │ ├── TCGA-CQ-5324-01A-01R-1686-07.rpkm │ ├── TCGA-CQ-5325-01A-01R-1686-07.rpkm │ ├── TCGA-CQ-5326-01A-01R-1873-07.rpkm │ ├── TCGA-CQ-5327-01A-01R-1686-07.rpkm │ ├── TCGA-CQ-5329-01A-01R-1686-07.rpkm │ ├── TCGA-CQ-5330-01A-01R-1686-07.rpkm │ ├── TCGA-CQ-5332-01A-01R-1686-07.rpkm │ ├── TCGA-CQ-5333-01A-01R-2403-07.rpkm │ ├── TCGA-CQ-6218-01A-11R-1915-07.rpkm │ ├── TCGA-CQ-6219-01A-11R-1915-07.rpkm │ ├── TCGA-CQ-6220-01A-11R-1915-07.rpkm │ ├── TCGA-CQ-6221-01A-11R-2081-07.rpkm │ ├── TCGA-CQ-6222-01A-11R-1915-07.rpkm │ ├── TCGA-CQ-6223-01A-11R-1915-07.rpkm │ ├── TCGA-CQ-6224-01A-11R-1915-07.rpkm │ ├── TCGA-CQ-6225-01A-11R-1915-07.rpkm │ ├── TCGA-CQ-6228-01A-11R-1915-07.rpkm │ ├── TCGA-CQ-6229-01A-11R-1915-07.rpkm │ ├── TCGA-CQ-7063-01A-11R-2403-07.rpkm │ ├── TCGA-CQ-7065-01A-11R-2081-07.rpkm │ ├── TCGA-CQ-7067-01A-11R-2232-07.rpkm │ ├── TCGA-CQ-7068-01A-11R-2081-07.rpkm │ ├── TCGA-CQ-7069-01A-11R-2403-07.rpkm │ ├── TCGA-CQ-7071-01A-12R-A30B-07.rpkm │ ├── TCGA-CQ-7072-01A-21R-A30B-07.rpkm │ ├── TCGA-CQ-A4C6-01A-11R-A24Z-07.rpkm │ ├── TCGA-CQ-A4C7-01A-11R-A24Z-07.rpkm │ ├── TCGA-CQ-A4C9-01A-11R-A24Z-07.rpkm │ ├── TCGA-CQ-A4CA-01A-11R-A24Z-07.rpkm │ ├── TCGA-CQ-A4CB-01A-11R-A24Z-07.rpkm │ ├── TCGA-CQ-A4CD-01A-21R-A24Z-07.rpkm │ ├── TCGA-CQ-A4CE-01A-11R-A266-07.rpkm │ ├── TCGA-CQ-A4CG-01A-11R-A266-07.rpkm │ ├── TCGA-CQ-A4CH-01A-11R-A266-07.rpkm │ ├── TCGA-CQ-A4CI-01A-11R-A266-07.rpkm │ ├── TCGA-CR-5243-01A-01R-1514-07.rpkm │ ├── TCGA-CR-5247-01A-01R-2016-07.rpkm │ ├── TCGA-CR-5249-01A-01R-1514-07.rpkm │ ├── TCGA-CR-5250-01A-01R-1514-07.rpkm │ ├── TCGA-CR-6467-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6471-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6472-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6474-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6477-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6478-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6480-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6481-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6482-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6484-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6487-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6488-01A-12R-2081-07.rpkm │ ├── TCGA-CR-6491-01A-11R-1873-07.rpkm │ ├── TCGA-CR-6493-01A-11R-1873-07.rpkm │ ├── TCGA-CR-7364-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7365-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7367-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7368-01A-11R-2132-07.rpkm │ ├── TCGA-CR-7369-01A-11R-2132-07.rpkm │ ├── TCGA-CR-7370-01A-11R-2132-07.rpkm │ ├── TCGA-CR-7371-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7372-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7373-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7374-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7376-01A-11R-2132-07.rpkm │ ├── TCGA-CR-7377-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7379-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7380-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7382-01A-11R-2132-07.rpkm │ ├── TCGA-CR-7383-01A-11R-2132-07.rpkm │ ├── TCGA-CR-7385-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7386-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7389-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7390-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7391-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7392-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7395-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7397-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7398-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7399-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7401-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7402-01A-11R-2016-07.rpkm │ ├── TCGA-CR-7404-01A-11R-2132-07.rpkm │ ├── TCGA-CV-5430-01A-02R-1686-07.rpkm │ ├── TCGA-CV-5431-01A-01R-1514-07.rpkm │ ├── TCGA-CV-5432-01A-02R-1686-07.rpkm │ ├── TCGA-CV-5434-01A-01R-1686-07.rpkm │ ├── TCGA-CV-5435-01A-01R-1686-07.rpkm │ ├── TCGA-CV-5436-01A-01R-1514-07.rpkm │ ├── TCGA-CV-5439-01A-01R-1686-07.rpkm │ ├── TCGA-CV-5440-01A-01R-1514-07.rpkm │ ├── TCGA-CV-5442-01A-01R-1514-07.rpkm │ ├── TCGA-CV-5443-01A-01R-1514-07.rpkm │ ├── TCGA-CV-5444-01A-02R-1514-07.rpkm │ ├── TCGA-CV-5966-01A-11R-1686-07.rpkm │ ├── TCGA-CV-5970-01A-11R-1686-07.rpkm │ ├── TCGA-CV-5971-01A-11R-1686-07.rpkm │ ├── TCGA-CV-5973-01A-11R-1686-07.rpkm │ ├── TCGA-CV-5976-01A-11R-1686-07.rpkm │ ├── TCGA-CV-5977-01A-11R-1686-07.rpkm │ ├── TCGA-CV-5978-01A-11R-1686-07.rpkm │ ├── TCGA-CV-5979-01A-11R-1686-07.rpkm │ ├── TCGA-CV-6003-01A-11R-1686-07.rpkm │ ├── TCGA-CV-6436-01A-11R-1686-07.rpkm │ ├── TCGA-CV-6441-01A-11R-1686-07.rpkm │ ├── TCGA-CV-6933-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6934-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6935-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6936-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6937-01A-11R-2016-07.rpkm │ ├── TCGA-CV-6938-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6939-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6940-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6942-01A-21R-2016-07.rpkm │ ├── TCGA-CV-6943-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6945-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6950-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6951-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6952-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6953-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6954-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6955-01A-11R-2016-07.rpkm │ ├── TCGA-CV-6956-01A-21R-2016-07.rpkm │ ├── TCGA-CV-6959-01A-11R-1915-07.rpkm │ ├── TCGA-CV-6960-01A-41R-2016-07.rpkm │ ├── TCGA-CV-6961-01A-21R-1915-07.rpkm │ ├── TCGA-CV-6962-01A-11R-1915-07.rpkm │ ├── TCGA-CV-7089-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7090-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7091-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7095-01A-21R-2016-07.rpkm │ ├── TCGA-CV-7097-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7099-01A-41R-2016-07.rpkm │ ├── TCGA-CV-7100-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7101-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7102-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7103-01A-21R-2016-07.rpkm │ ├── TCGA-CV-7104-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7177-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7178-01A-21R-2016-07.rpkm │ ├── TCGA-CV-7180-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7183-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7235-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7236-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7238-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7242-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7243-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7247-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7248-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7250-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7252-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7253-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7254-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7255-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7261-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7263-01A-11R-2016-07.rpkm │ ├── TCGA-CV-7406-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7407-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7409-01A-31R-2232-07.rpkm │ ├── TCGA-CV-7410-01A-21R-2081-07.rpkm │ ├── TCGA-CV-7411-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7413-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7414-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7416-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7418-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7421-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7423-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7424-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7425-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7427-01A-11R-2081-07.rpkm │ ├── TCGA-CV-7428-01A-11R-2132-07.rpkm │ ├── TCGA-CV-7429-01A-11R-2132-07.rpkm │ ├── TCGA-CV-7430-01A-11R-2132-07.rpkm │ ├── TCGA-CV-7432-01A-11R-2132-07.rpkm │ ├── TCGA-CV-7433-01A-11R-2132-07.rpkm │ ├── TCGA-CV-7434-01A-11R-2132-07.rpkm │ ├── TCGA-CV-7437-01A-21R-2132-07.rpkm │ ├── TCGA-CV-7440-01A-11R-2132-07.rpkm │ ├── TCGA-CV-A45O-01A-21R-A24H-07.rpkm │ ├── TCGA-CV-A45P-01A-11R-A24H-07.rpkm │ ├── TCGA-CV-A45Q-01A-11R-A24H-07.rpkm │ ├── TCGA-CV-A45R-01A-11R-A24H-07.rpkm │ ├── TCGA-CV-A45T-01A-11R-A24H-07.rpkm │ ├── TCGA-CV-A45U-01A-12R-A24H-07.rpkm │ ├── TCGA-CV-A45V-01A-21R-A24Z-07.rpkm │ ├── TCGA-CV-A45W-01A-11R-A24Z-07.rpkm │ ├── TCGA-CV-A45X-01A-21R-A24Z-07.rpkm │ ├── TCGA-CV-A45Y-01A-11R-A24Z-07.rpkm │ ├── TCGA-CV-A45Z-01A-21R-A24Z-07.rpkm │ ├── TCGA-CV-A460-01A-21R-A24Z-07.rpkm │ ├── TCGA-CV-A461-01A-41R-A266-07.rpkm │ ├── TCGA-CV-A463-01A-11R-A266-07.rpkm │ ├── TCGA-CV-A464-01A-11R-A266-07.rpkm │ ├── TCGA-CV-A465-01A-11R-A266-07.rpkm │ ├── TCGA-CV-A468-01A-11R-A266-07.rpkm │ ├── TCGA-CV-A6JD-01A-11R-A31N-07.rpkm │ ├── TCGA-CV-A6JE-01A-11R-A31N-07.rpkm │ ├── TCGA-CV-A6JM-01A-11R-A31N-07.rpkm │ ├── TCGA-CV-A6JN-01A-11R-A31N-07.rpkm │ ├── TCGA-CV-A6JO-01B-11R-A34R-07.rpkm │ ├── TCGA-CV-A6JU-01A-11R-A31N-07.rpkm │ ├── TCGA-CV-A6JY-01A-11R-A31N-07.rpkm │ ├── TCGA-CV-A6JZ-01A-11R-A31N-07.rpkm │ ├── TCGA-CV-A6K1-01A-11R-A31N-07.rpkm │ ├── TCGA-CX-7082-01A-11R-2016-07.rpkm │ ├── TCGA-CX-7085-01A-21R-2016-07.rpkm │ ├── TCGA-CX-7086-01A-11R-2081-07.rpkm │ ├── TCGA-CX-7219-01A-11R-2016-07.rpkm │ ├── TCGA-CX-A4AQ-01A-11R-A24Z-07.rpkm │ ├── TCGA-D6-6515-01A-21R-1873-07.rpkm │ ├── TCGA-D6-6823-01A-11R-1915-07.rpkm │ ├── TCGA-D6-6824-01A-11R-1915-07.rpkm │ ├── TCGA-D6-6825-01A-21R-1915-07.rpkm │ ├── TCGA-D6-6826-01A-11R-1915-07.rpkm │ ├── TCGA-D6-6827-01A-11R-1915-07.rpkm │ ├── TCGA-D6-8568-01A-11R-2403-07.rpkm │ ├── TCGA-D6-8569-01A-11R-2403-07.rpkm │ ├── TCGA-D6-A4Z9-01A-11R-A24Z-07.rpkm │ ├── TCGA-D6-A4ZB-01A-11R-A24Z-07.rpkm │ ├── TCGA-D6-A6EK-01A-11R-A31N-07.rpkm │ ├── TCGA-D6-A6EM-01A-21R-A31N-07.rpkm │ ├── TCGA-D6-A6EN-01A-11R-A31N-07.rpkm │ ├── TCGA-D6-A6EO-01A-11R-A31N-07.rpkm │ ├── TCGA-D6-A6EP-01A-11R-A31N-07.rpkm │ ├── TCGA-D6-A6ES-01A-12R-A31N-07.rpkm │ ├── TCGA-D6-A74Q-01A-11R-A34R-07.rpkm │ ├── TCGA-DQ-5624-01A-01R-1873-07.rpkm │ ├── TCGA-DQ-5625-01A-01R-1873-07.rpkm │ ├── TCGA-DQ-5629-01A-01R-1873-07.rpkm │ ├── TCGA-DQ-5630-01A-01R-1873-07.rpkm │ ├── TCGA-DQ-7588-01A-11R-2081-07.rpkm │ ├── TCGA-DQ-7589-01A-11R-2232-07.rpkm │ ├── TCGA-DQ-7590-01A-11R-2232-07.rpkm │ ├── TCGA-DQ-7591-01A-11R-2081-07.rpkm │ ├── TCGA-DQ-7592-01A-11R-2081-07.rpkm │ ├── TCGA-DQ-7593-01A-11R-2232-07.rpkm │ ├── TCGA-DQ-7594-01A-11R-2232-07.rpkm │ ├── TCGA-DQ-7595-01A-11R-2232-07.rpkm │ ├── TCGA-DQ-7596-01A-11R-2232-07.rpkm │ ├── TCGA-F7-8298-01A-11R-2403-07.rpkm │ ├── TCGA-F7-8489-01A-31R-2403-07.rpkm │ ├── TCGA-F7-A50G-01A-11R-A266-07.rpkm │ ├── TCGA-F7-A50I-01A-11R-A28V-07.rpkm │ ├── TCGA-F7-A50J-01A-21R-A28V-07.rpkm │ ├── TCGA-F7-A61S-01A-11R-A28V-07.rpkm │ ├── TCGA-F7-A61V-01A-11R-A28V-07.rpkm │ ├── TCGA-F7-A61W-01A-11R-A28V-07.rpkm │ ├── TCGA-F7-A620-01A-11R-A28V-07.rpkm │ ├── TCGA-F7-A622-01A-11R-A28V-07.rpkm │ ├── TCGA-F7-A623-01A-11R-A28V-07.rpkm │ ├── TCGA-F7-A624-01A-22R-A30B-07.rpkm │ ├── TCGA-H7-7774-01A-21R-2081-07.rpkm │ ├── TCGA-H7-8501-01A-11R-2403-07.rpkm │ ├── TCGA-H7-8502-01A-11R-2403-07.rpkm │ ├── TCGA-H7-A6C4-01A-11R-A30B-07.rpkm │ ├── TCGA-H7-A76A-01A-51R-A34R-07.rpkm │ ├── TCGA-HD-7229-01A-11R-2016-07.rpkm │ ├── TCGA-HD-7753-01A-11R-2081-07.rpkm │ ├── TCGA-HD-7754-01A-11R-2081-07.rpkm │ ├── TCGA-HD-7917-01A-11R-2232-07.rpkm │ ├── TCGA-HD-8224-01A-11R-2403-07.rpkm │ ├── TCGA-HD-8314-01A-11R-2403-07.rpkm │ ├── TCGA-HD-8634-01A-11R-2403-07.rpkm │ ├── TCGA-HD-8635-01A-11R-2403-07.rpkm │ ├── TCGA-HD-A4C1-01A-11R-A24H-07.rpkm │ ├── TCGA-HD-A633-01A-11R-A28V-07.rpkm │ ├── TCGA-HD-A634-01A-11R-A28V-07.rpkm │ ├── TCGA-HD-A6I0-01A-11R-A31N-07.rpkm │ ├── TCGA-HL-7533-01A-11R-2232-07.rpkm │ ├── TCGA-IQ-7630-01A-11R-2081-07.rpkm │ ├── TCGA-IQ-7631-01A-11R-2081-07.rpkm │ ├── TCGA-IQ-7632-01A-11R-2081-07.rpkm │ ├── TCGA-IQ-A61E-01A-22R-A30B-07.rpkm │ ├── TCGA-IQ-A61G-01A-11R-A30B-07.rpkm │ ├── TCGA-IQ-A61H-01A-11R-A30B-07.rpkm │ ├── TCGA-IQ-A61I-01A-11R-A30B-07.rpkm │ ├── TCGA-IQ-A61J-01A-11R-A30B-07.rpkm │ ├── TCGA-IQ-A61O-01A-11R-A30B-07.rpkm │ ├── TCGA-IQ-A6SG-01A-12R-A34R-07.rpkm │ ├── TCGA-IQ-A6SH-01A-12R-A34R-07.rpkm │ ├── TCGA-KU-A66S-01A-21R-A30B-07.rpkm │ ├── TCGA-KU-A66T-01A-11R-A30B-07.rpkm │ ├── TCGA-KU-A6H7-01A-11R-A31N-07.rpkm │ ├── TCGA-KU-A6H8-01A-21R-A34R-07.rpkm │ ├── TCGA-MT-A51W-01A-21R-A266-07.rpkm │ ├── TCGA-MT-A51X-01A-11R-A266-07.rpkm │ ├── TCGA-MT-A67A-01A-11R-A30B-07.rpkm │ ├── TCGA-MT-A67D-01A-31R-A30B-07.rpkm │ ├── TCGA-MT-A67F-01A-11R-A30B-07.rpkm │ ├── TCGA-MT-A7BN-01A-12R-A34R-07.rpkm │ ├── TCGA-MZ-A5BI-01A-31R-A34R-07.rpkm │ ├── TCGA-MZ-A6I9-01A-11R-A31N-07.rpkm │ ├── TCGA-MZ-A7D7-01A-21R-A34R-07.rpkm │ ├── TCGA-P3-A5Q5-01A-11R-A28V-07.rpkm │ ├── TCGA-P3-A5Q6-01A-11R-A28V-07.rpkm │ ├── TCGA-P3-A5QA-01A-11R-A28V-07.rpkm │ ├── TCGA-P3-A5QE-01A-11R-A28V-07.rpkm │ ├── TCGA-P3-A5QF-01A-11R-A28V-07.rpkm │ ├── TCGA-P3-A6SW-01A-11R-A34R-07.rpkm │ ├── TCGA-P3-A6SX-01A-11R-A34R-07.rpkm │ ├── TCGA-P3-A6T0-01A-12R-A34R-07.rpkm │ ├── TCGA-P3-A6T2-01A-11R-A34R-07.rpkm │ ├── TCGA-P3-A6T3-01A-11R-A34R-07.rpkm │ ├── TCGA-P3-A6T4-01A-11R-A34R-07.rpkm │ ├── TCGA-P3-A6T5-01A-11R-A34R-07.rpkm │ ├── TCGA-P3-A6T6-01A-11R-A34R-07.rpkm │ ├── TCGA-P3-A6T7-01A-11R-A34R-07.rpkm │ ├── TCGA-P3-A6T8-01A-11R-A34R-07.rpkm │ ├── TCGA-QK-A64Z-01A-11R-A30B-07.rpkm │ ├── TCGA-QK-A652-01A-11R-A30B-07.rpkm │ ├── TCGA-QK-A6IH-01A-11R-A31N-07.rpkm │ ├── TCGA-QK-A6II-01A-11R-A31N-07.rpkm │ ├── TCGA-QK-A6IJ-01A-11R-A31N-07.rpkm │ ├── TCGA-QK-A6V9-01A-11R-A34R-07.rpkm │ ├── TCGA-QK-A6VB-01A-12R-A34R-07.rpkm │ ├── TCGA-QK-A6VC-01A-23R-A34R-07.rpkm │ ├── TCGA-RS-A6TO-01A-32R-A34R-07.rpkm │ ├── TCGA-RS-A6TP-01A-12R-A34R-07.rpkm │ ├── TCGA-T2-A6WX-01A-12R-A34R-07.rpkm │ ├── TCGA-T2-A6WZ-01A-21R-A34R-07.rpkm │ ├── TCGA-T2-A6X0-01A-11R-A34R-07.rpkm │ ├── TCGA-T2-A6X2-01A-12R-A34R-07.rpkm │ ├── TCGA-TN-A7HI-01A-11R-A34R-07.rpkm │ ├── TCGA-TN-A7HJ-01A-12R-A34R-07.rpkm │ ├── TCGA-TN-A7HL-01A-11R-A34R-07.rpkm │ ├── TCGA-UF-A718-01A-22R-A34R-07.rpkm │ ├── TCGA-UF-A719-01A-12R-A34R-07.rpkm │ ├── TCGA-UF-A71A-01A-22R-A34R-07.rpkm │ ├── TCGA-UF-A71B-01A-12R-A34R-07.rpkm │ ├── TCGA-UF-A71D-01A-12R-A34R-07.rpkm │ ├── TCGA-UF-A71E-01A-31R-A34R-07.rpkm │ ├── TCGA-UF-A7J9-01A-12R-A34R-07.rpkm │ ├── TCGA-UF-A7JA-01A-12R-A34R-07.rpkm │ ├── TCGA-UF-A7JC-01A-21R-A34R-07.rpkm │ ├── TCGA-UF-A7JD-01A-11R-A34R-07.rpkm │ ├── TCGA-UF-A7JF-01A-11R-A34R-07.rpkm │ ├── TCGA-UF-A7JJ-01A-11R-A34R-07.rpkm │ ├── TCGA-UF-A7JK-01A-11R-A34R-07.rpkm │ ├── TCGA-UF-A7JO-01A-11R-A34R-07.rpkm │ ├── TCGA-UF-A7JS-01A-11R-A34R-07.rpkm │ ├── TCGA-UF-A7JT-01A-11R-A34R-07.rpkm │ ├── TCGA-UF-A7JV-01A-11R-A34R-07.rpkm │ ├── TCGA-UP-A6WW-01A-12R-A34R-07.rpkm │ ├── TCGA-WA-A7GZ-01A-11R-A34R-07.rpkm │ └── TCGA-WA-A7H4-01A-21R-A34R-07.rpkm ├── M_RSEM_Expression ├── 1_get_data.sh ├── 2_make_BED.sh ├── 3_parse_RSEM.sh ├── 4_stream_exons.sh ├── 5_evaluate_expression_Pvalue.sh ├── BPS_Stage.config ├── README.md └── dat │ ├── BED │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.exons.bed │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.exons.stream.bed │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.genes.bed │ ├── FDR │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.gene.pval.FDR.dat │ ├── NeighborSummary.dat │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.RSEM.dat ├── N_DrawBreakpoint ├── 1_draw_PindelRP.sh ├── 2_draw_Discordant.sh ├── 3_draw_Contig.sh ├── 4_draw_novoBreak.sh ├── BPS_Stage.config ├── README.md ├── TODO.txt └── dat │ ├── GGP │ ├── GGP.Contig │ └── TCGA-BA-4077-01B-01D-2268-08 │ │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.Breakpoints.ggp │ ├── GGP.Discordant │ └── TCGA-BA-4077-01B-01D-2268-08 │ │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.Breakpoints.ggp │ ├── GGP.PindelRP │ └── TCGA-BA-4077-01B-01D-2268-08 │ │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.Breakpoints.ggp │ └── GGP.novoBreak │ └── TCGA-BA-4077-01B-01D-2268-08 │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.Breakpoints.ggp ├── O_DrawDepth ├── 1_make_depth_ggp.sh ├── 2_add_CBS.sh ├── 3_add_PindelRP.sh ├── 4_add_Discordant.sh ├── 5_add_Contig.sh ├── BPS_Stage.config ├── README.md └── dat │ ├── GGP │ ├── GGP.CBS │ └── TCGA-BA-4077-01B-01D-2268-08 │ │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.A.depth.ggp │ │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.depth.ggp │ ├── GGP.Contig │ └── TCGA-BA-4077-01B-01D-2268-08 │ │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.A.depth.ggp │ │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.depth.ggp │ ├── GGP.Depth │ └── TCGA-BA-4077-01B-01D-2268-08 │ │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.A.depth.ggp │ │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.depth.ggp │ ├── GGP.Discordant │ └── TCGA-BA-4077-01B-01D-2268-08 │ │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.A.depth.ggp │ │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.depth.ggp │ └── GGP.PindelRP │ └── TCGA-BA-4077-01B-01D-2268-08 │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.A.depth.ggp │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.B.depth.ggp ├── P_DrawAnnotation ├── 1_make_annotation_ggp.sh ├── BPS_Stage.config ├── README.md └── dat │ └── GGP │ └── TCGA-BA-4077-01B-01D-2268-08 │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.chrom.B.annotation.ggp ├── Q_DrawHistogram ├── 1_make_histogram_ggp.sh ├── BPS_Stage.config ├── README.md └── dat │ └── GGP │ └── TCGA-BA-4077-01B-01D-2268-08 │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.50K.histogram.ggp │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.histogram.ggp ├── README.md ├── T_PlotStructure ├── 1_drawBreakpointPlots.sh ├── 2_make_png.sh ├── BPS_Stage.config ├── README.md └── plots │ ├── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.BreakpointSurvey.pdf │ └── TCGA-BA-4077-01B-01D-2268-08.AA.chr14.BreakpointSurvey.png ├── U_PlotExpression ├── 1_plot_RPKM_Pval_bubble.sh ├── 2_plot_RSEM_Pval_bubble.sh ├── 3_make_png.sh ├── BPS_Stage.config ├── README.md └── plots │ ├── 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