hg19.json~

 {"references": {
    "BWAGENOME": "/fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa",
    "GENOME": "/fdb/GATK_resource_bundle/b37/human_g1k_v37.fasta",
    "INDELSITES": "/fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf", 
    "NOVOINDEX": "/data/CCBR/local/lib/human_g1k_v37_iupac.nix", 
    "REFFLAT": "/data/CCBR/local/lib/SS_exome.bed", 
    "SNPSITES": "/fdb/GATK_resource_bundle/b37/dbsnp_138.b37.vcf",
    "INDELSITES2":"/fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
#    "ANNDIR": "/usr/local/apps/ANNOVAR/2014-11-12/humandb/",
    "ANNDIR": "/data/CCBR/local/lib/AnnovarDB/",

    "tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg19-2.8/Mills_and_1000G_gold_standard.indels.hg19.vcf.gz",
    "tg_PHASE_INDELS": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_phase1.indels.hg19.vcf.gz",
    "SNP138": "/fdb/GATK_resource_bundle/hg19-2.8/dbsnp_138.hg19.vcf.gz",
    "HAPMAP": "/fdb/GATK_resource_bundle/hg19-2.8/hapmap_3.3.hg19.vcf.gz",
    "B1K": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_phase1.snps.high_confidence.hg19.vcf.gz",
    "OMNI": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_omni2.5.hg19.vcf.gz", 
    "adapter.file": "/data/CCBR/dev/Pipeline/Pipeliner/Data/TruSeq_and_nextera_adapters.ngsqc.dat",
    "fastqc.adapters": "/data/CCBR/dev/Pipeline/Pipeliner/Data/fastqc.adapters",
    "trimmomatic.adapters": "/data/CCBR/dev/Pipeline/Pipeliner/Data/adapters2.fa",
    "ORGANISM": "HUMAN",
    "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", 
    "ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
    "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
    "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
    "gencodeGtf":"gencode.vM4.all.gtf",
    "genomeRnaseq": "GRCm38.p3.genome.fa",
    "genomeDir": "/data/CCBR/local/lib/genomes",
    "gtfDir": "/data/CCBR/local/lib/gtf",
    "genomeDir2": "/data/CCBR/local/lib/genomes/2pass",
    "gtfERCC": "gencode.vM4.all_ERCC.gtf",
    "genomeRnaseqErcc": "GRCm38.p3.ERCC.genome.fa",
    "DB29": "/data/CCBR/local/lib/snpEff_db/dbNSFP2.9.txt.gz",
    "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.1c/snpEff.config",
#    "FILTERSIFT": "(FILTER='PASS') & ( QUAL >= 20 )",
    "FILTERSIFT": "( QUAL >= 20 )",
    "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF",
    "SNPEFF_GENOME": "GRCh37.75",
    "HAPMAP_DBNSFP": "/data/CCBR/local/lib/snpEff_db/hapmap.bed",
    "REGULOMEDB": "/data/CCBR/local/lib/snpEff_db/RegulomeDB.bed",
    "MUTECTCOSMIC": "/fdb/muTect/cosmic_v67.b37.vcf",
    "MUTECTSNP": "--dbsnp /fdb/muTect/dbsnp_137.b37.vcf",
    "MUTECTGENOME": "/fdb/muTect/human_g1k_v37.fasta"
        }
}