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GATK_workflow2.json
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{
"GATK_test.ref_index": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.fai",
"GATK_test.ref_bwt": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.bwt",
"GATK_test.ref_fasta": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta",
"GATK_test.PICARD": "/work-z/user/guoh/soft/picard/build/libs/picard.jar",
"GATK_test.fastq_directory_path": "/work-z/user/guoh/testData/WES/giab_NA12878_Garvan",
"GATK_test.ref_pac": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.pac",
"GATK_test.ref_sa": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.sa",
"GATK_test.ref_ann": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.ann",
"GATK_test.ref_amb": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.fasta.amb",
"GATK_test.SAMTOOLS131": "/work-z/user/guoh/soft/samtools-1.3.1/samtools",
"GATK_test.sampleMetainfo": "/work-z/user/guoh/research/2016-10-12-Shanghai9thHospital-Tongue_cancer/sample.fastqinfo_check.tsv",
"GATK_test.BWA0712": "/work-z/user/guoh/soft/bwa-0.7.12/bwa",
"GATK_test.ref_dict": "/work-a/public/gatk_bundle/2.8/hg19/ucsc.hg19.dict",
"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.GATK36": "/work-z/user/guoh/soft/GenomeAnalysisTK.jar",
"GATK_test.gold_indels": "/work-a/public/gatk_bundle/2.8/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf",
"GATK_test.dbSNP_vcf": "/work-a/public/gatk_bundle/2.8/hg19/dbsnp_138.hg19.vcf",
"GATK_test.dbSNP_vcf_index": "/work-a/public/gatk_bundle/2.8/hg19/dbsnp_138.hg19.vcf.idx",
"GATK_test.THREAD_NUM": "18",
"GATK_test.FinalBams": 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