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varscan3.json
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varscan3.json
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{"mpileup_varscan.THREAD_NUM": "18", "mpileup_varscan.panel_bed": "medexome", "mpileup_varscan.ref_amb": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.amb", "mpileup_varscan.RawBams": [["S1_I3-35749-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I3-35749-Tumor.bam"], ["S1_I4-35749-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I4-35749-Normal.bam"], ["S1_I5-789918-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I5-789918-Tumor.bam"], ["S1_I6-789918-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I6-789918-Normal.bam"], ["S1_I7-739142-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I7-739142-Tumor.bam"], ["S1_I8-739142-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I8-739142-Normal.bam"], ["S1_I9-752703-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I9-752703-Tumor.bam"], ["S1_I10-752703-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I10-752703-Normal.bam"], ["S1_I11-753648-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I11-753648-Tumor.bam"], ["S1_I12-753648-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I12-753648-Normal.bam"], ["S1_I13-717145-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I13-717145-Tumor.bam"], ["S1_I14-717145-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S1_I14-717145-Normal.bam"], ["S2_I15-738908-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S2_I15-738908-Tumor.bam"], ["S2_I16-738908-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S2_I16-738908-Normal.bam"], ["S2_I17-719306-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S2_I17-719306-Tumor.bam"], ["S2_I18-719306-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S2_I18-719306-Normal.bam"], ["S4_I35-746124-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S4_I35-746124-Tumor.bam"], ["S4_I36-746124-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S4_I36-746124-Normal.bam"], ["S5_I37-754462-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S5_I37-754462-Tumor.bam"], ["S5_I38-754462-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S5_I38-754462-Normal.bam"], ["S5_I39-835346-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S5_I39-835346-Tumor.bam"], ["S5_I40-835346-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S5_I40-835346-Normal.bam"], ["S5_I41-829958-Tumor", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S5_I41-829958-Tumor.bam"], ["S5_I42-829958-Normal", "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/Data/BwaMem/S5_I42-829958-Normal.bam"]], "mpileup_varscan.BWA0712": "/work-z/user/guoh/soft/bwa-0.7.12/bwa", "mpileup_varscan.ref_pac": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.pac", "mpileup_varscan.GATK36": "/work-z/user/guoh/soft/GenomeAnalysisTK.jar", "mpileup_varscan.ref_bwt": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.bwt", "mpileup_varscan.ref_ann": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.ann", "mpileup_varscan.PICARD": "/work-z/user/guoh/soft/picard/build/libs/picard.jar", "mpileup_varscan.sampleMetainfo": "/work-z/user/guoh/research/2016-11-04-Shanghai9thHospital-Tongue_cancer2/sample.fastqinfo.tsv", "mpileup_varscan.ref_fasta": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta", "mpileup_varscan.ref_sa": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.sa", "mpileup_varscan.ref_index": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.fai", "mpileup_varscan.ref_dict": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.dict", "mpileup_varscan.VarScan": "/work-a/app/varscan-2.4.2/VarScan.v2.4.2.jar", "mpileup_varscan.SAMTOOLS131": "/work-z/user/guoh/soft/samtools-1.3.1/samtools"}