mm10.json

 {"references": {
    "exomeseq": {
    "BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa",
    "GENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
    "CHROMS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_chromosomes",
    "INDELSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/sorted.dict.repaired_mgp.v5.merged.indels.dbSNP142.normed.vcf",
    "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_dbSNP_allStrains_compSet.vcf",
    "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_genome.nix", 
    "SNPSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",
    "adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
    "fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
    "trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
    "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", 
    "ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
    "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
    "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
    "ORGANISM": "MOUSE",
    "SNP138": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",
    "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/SS_mouse_exome_mm10_reformat.bed",
    "SNPEFF_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/snpEff.config",
    "SNPEFF_GENOME": "GRCm38.82",
    "FILTERSIFT": "( QUAL >= 20 )",
    "MUTECTGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
    "MUTECTVARIANTS": "--dbsnp /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",
    "STRELKA_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/strelka_demo_config.ini",
    "DELLY_EXCLUSIONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/delly.mouse.mm10.excl.tsv",
    "CNVKIT_TARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_cnvkit_targets_split.bed",
    "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",    
    #below here is junk placeholders
    "HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
    "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",
    "DB29": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/dbNSFP2.9.txt.gz",
    "MUTECTCOSMIC": "",
    "MUTECTSNP": ""
},
    "genomeseq": {
    "BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa",
    "GENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
    "CHROMS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_chromosomes",
    "INDELSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/sorted.dict.repaired_mgp.v5.merged.indels.dbSNP142.normed.vcf",
    "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_dbSNP_allStrains_compSet.vcf",
    "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_genome.nix", 
    "SNPSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",
    "adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
    "fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
    "trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
    "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", 
    "ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
    "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
    "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
    "ORGANISM": "MOUSE",
    "SNP138": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",
    "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/SS_mouse_exome_mm10_reformat.bed",
    "SNPEFF_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/snpEff.config",
    "SNPEFF_GENOME": "GRCm38.82",
    "FILTERSIFT": "( QUAL >= 20 )",
    "MUTECTGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
    "MUTECTVARIANTS": "--dbsnp /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",
    "STRELKA_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/strelka_demo_config.ini",
    "DELLY_EXCLUSIONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/delly.mouse.mm10.excl.tsv",
    "CNVKIT_TARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_cnvkit_targets_split.bed",
    "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",    
    #below here is junk placeholders
    "HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
    "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",
    "DB29": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/dbNSFP2.9.txt.gz",
    "MUTECTCOSMIC": "",
    "MUTECTSNP": ""
},
     "rnaseq":{
"GENOMEFILE": "/fdb/STAR_2.4.2a/GENCODE/Gencode_mouse/release_M4/ref.fa",	 
"GTFFILE": "/fdb/STAR_2.4.2a/GENCODE/Gencode_mouse/release_M4/genes.gtf",
"STARDIR": "/fdb/STAR_2.4.2a/GENCODE/Gencode_mouse/release_M4/genes-",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/dev/Mm10_genes.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/dev/refFlatMm10.txt",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/dev/rsemref/mouse_gencode",
"SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/dev/rsemref/mouse_gencode.transcripts.fa",
"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/Mm10.rRNA.interval_list_v3"

},
 }

 }