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Copy pathGATK_workflow_pedigree.json
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GATK_workflow_pedigree.json
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{"GATK_test.ref_dict": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.dict", "GATK_test.ref_index": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.fai", "GATK_test.SAMTOOLS131": "/work-z/user/guoh/soft/samtools-1.3.1/samtools", "GATK_test.dbSNP_vcf_index": "/work-a/public/gatk_bundle/2.8/hg19/dbsnp_138.hg19.vcf.idx", "GATK_test.sampleMetainfo": "/work-z/user/guoh/research/2016-12-28-PedigreeCancerWGS/sample_fastqinfo.tsv", "GATK_test.ref_pac": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.pac", "GATK_test.ref_ann": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.ann", "GATK_test.THREAD_NUM": "18", "GATK_test.BWA0712": "/work-z/user/guoh/soft/bwa-0.7.12/bwa", "GATK_test.ref_amb": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.amb", "GATK_test.ref_bwt": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.bwt", "GATK_test.gold_indels_index": "/work-a/public/gatk_bundle/2.8/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx", "GATK_test.ref_sa": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.sa", "GATK_test.PICARD": "/work-z/user/guoh/soft/picard/build/libs/picard.jar", "GATK_test.dbSNP_vcf": "/work-a/public/gatk_bundle/2.8/hg19/dbsnp_138.hg19.vcf", "GATK_test.ref_fasta": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta", "GATK_test.GATK36": "/work-z/user/guoh/soft/GenomeAnalysisTK.jar", "GATK_test.fastq_directory_path": "/work-z/user/guoh/testData/WES/giab_NA12878_Garvan", "GATK_test.gold_indels": "/work-a/public/gatk_bundle/2.8/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf"}