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mm10.json
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{"references": {
"exomeseq": {
"VARDICTBED": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10.chroms.bed",
"BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa",
"PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_dbSNP_allStrains_compSet.vcf.gz",
"GENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
"CHROMS": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chrX","chrY","chrM"],
"INDELSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
"KNOWNINDELS": "-known /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNVCF2": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_knownSNPs_sites.vcf.gz",
"NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_genome.nix",
"CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/genome.fa",
"CNVKITREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_flatRef.cnn",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mouse_genomes_strain_key.txt",
"ADMIXTUREREFS": "39",
"SNPSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
"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",
"ALVIEWGENOME": "mm10",
"AVIASET": "mm10",
"SNP138": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/SS_mouse_exome_mm10_reformat.bed",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
"SNPEFF_GENOME": "GRCm38.86",
"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.gz",
"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",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-mm10.bed",
"CONPAIRMARKERSA": "/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_Mouse_All_Exon_V1_GRCm38_markers_MAF_0.4_LD_0.8.txt",
"CONPAIRMARKERSB": "/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_Mouse_All_Exon_V1_GRCm38_markers_MAF_0.4_LD_0.8.bed",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_UCSCexons.bed",
"THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_theta_SNPfile_reformat.txt",
"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": "",
"VEPBUILD": "GRCm38",
"VEPSPECIES": "mus_musculus",
"VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
"VEPGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/genome.fa",
"CANVASGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/mm10/WholeGenomeFasta",
"CANVASKMER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/mm10/mm10_kmer.fa",
"CANVASFILTER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/mm10/mm10_WindowMasker.bed",
"CANVASPLOIDY": "/data/CCBR_Pipeliner/db/PipeDB/lib/ploidy.vcf",
"CANVASBALLELES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_knownSNPs_sites.vcf.gz",
"CNVKITANNO": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_refFlat.txt",
},
"genomeseq": {
"VARDICTBED": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10.chroms.bed",
"PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_dbSNP_allStrains_compSet.vcf.gz",
"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/mm10_known_indels.vcf.gz",
"KNOWNINDELS": "-known /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNVCF2": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_knownSNPs_sites.vcf.gz",
"NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_genome.nix",
"CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/genome.fa",
"CNVKITREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_flatRef.cnn",
"CNVKITANTITARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/fake.antitargetcoverage.cnn",
"CNVKITWGSTARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_cnvkit_wgs_targets.bed",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mouse_genomes_strain_key.txt",
"ADMIXTUREREFS": "39",
"CNVKITANNO": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_refFlat.txt",
"CNVKITANTITARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/fake.antitargetcoverage.cnn",
"SNPSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
"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",
"ALVIEWGENOME": "mm10",
"AVIASET": "mm10",
"SNP138": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/SS_mouse_exome_mm10_reformat.bed",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
"SNPEFF_GENOME": "GRCm38.86",
"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.gz",
"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",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-mm10.bed",
"CONPAIRMARKERSA": "/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_Mouse_All_Exon_V1_GRCm38_markers_MAF_0.4_LD_0.8.txt",
"CONPAIRMARKERSB": "/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_Mouse_All_Exon_V1_GRCm38_markers_MAF_0.4_LD_0.8.bed",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_UCSCexons.bed",
"THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_theta_SNPfile_reformat.txt",
"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": "",
"VEPBUILD": "GRCm38",
"VEPSPECIES": "mus_musculus",
"CANVASGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/mm10/WholeGenomeFasta",
"CANVASKMER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/mm10/mm10_kmer.fa",
"CANVASFILTER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/mm10/mm10_WindowMasker.bed",
"CANVASPLOIDY": "/data/CCBR_Pipeliner/db/PipeDB/lib/ploidy.vcf",
"CANVASBALLELES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_knownSNPs_sites.vcf.gz",
"VEPBUILD": "GRCm38",
"VEPSPECIES": "mus_musculus",
"VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
"VEPGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/genome.fa",
},
"rnaseq":{
"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/mm10.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/genes.gtf",
"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/STAR/2.7.0f/genes-",
"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/qualimap_info.txt",
"KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/karyoplot_gene_coordinates.txt",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/annotate.genes.txt",
"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/annotate.isoforms.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/refFlat.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/genes.ref.bed",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/geneinfo.bed",
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/mm.vM12/",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/rsemref/mm10",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/mm10.rRNA_interval_list",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"FUSIONGTFFILE": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes.gtf",
"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/STAR/2.5.2b/genes-",
# "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/dev/rsemref/mouse_gencode",
# "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/dev/rsemref/mouse_gencode.transcripts.fa",
#"SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/mouse_gencode.transcripts.fa",
"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
"STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/Mouse_gencode_M20_CTAT_lib_Mar272019.plug-n-play/ctat_genome_lib_build_dir",
"FUSCATCHDAT": "/fdb/fusioncatcher/mus_musculus",
"FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fusioncatcher_mm10_configuration.cfg",
"ONCOFUSEBUILD": "mm10",
# "BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/mm10.fa",
# "CHROMS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_chromosomes",
# "INDELSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
"KNOWNINDELS": "-known /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNVCF2": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_knownSNPs_sites.vcf.gz",
# "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_genome.nix",
# "CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/genome.fa",
"SNPSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
"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",
"ALVIEWGENOME": "mm10",
"AVIASET": "mm10",
# "SNP138": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
"SNPEFF_GENOME": "GRCm38.86",
# "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.gz",
# "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",
# "CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-mm10.bed",
# "CONPAIRMARKERS": "/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_Mouse_All_Exon_V1_GRCm38_markers_MAF_0.4_LD_0.8.txt",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_UCSCexons.bed",
# "THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_theta_SNPfile_reformat.txt",
#below here is junk placeholders; touch at your peril
# "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": "",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mouse_genomes_strain_key.txt",
"ADMIXTUREREFS": "39",
},
"rnaseqvargerm": {
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/mm10.fa",
"GTFFILE": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes.gtf",
"STARDIR": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes-",
"STARREF": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes-",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/dev/Mm10_genes.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/dev/refFlatMm10.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCm38_mm10_RefSeq.bed",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/mouse_gencode",
"SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/mouse_gencode.transcripts.fa",
"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/gencode.vM12.annotation.rRNA.interval_list",
"BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/mm10.fa",
"CHROMS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_chromosomes",
"INDELSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
"KNOWNINDELS": "-known /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_indels.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"KNOWNVCF2": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_known_snps.vcf.gz",
"NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_genome.nix",
"CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/genome.fa",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/mouse_genomes_strain_key.txt",
"ADMIXTUREREFS": "39",
"SNPSITES": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
"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",
"ALVIEWGENOME": "mm10",
"AVIASET": "mm10",
"SNP138": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf.gz",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
"SNPEFF_GENOME": "GRCm38.86",
"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.gz",
"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",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-mm10.bed",
"CONPAIRMARKERS": "/data/CCBR_Pipeliner/db/PipeDB/lib/SureSelect_Mouse_All_Exon_V1_GRCm38_markers_MAF_0.4_LD_0.8.txt",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_UCSCexons.bed",
"THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_theta_SNPfile_reformat.txt",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
#below here is junk placeholders; touch at your peril
"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": ""
},
"mirseq":{
"BOWTIE_REF": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/bowtie_indices/mm10",
"FASTA_REF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/mm10_basic.fa",
"MIRBASE_MATURE": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/miRBase_v22/mmu_mature.fa",
"MIRBASE_HAIRPIN": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/miRBase_v22/mmu_hairpin.fa",
"ORGANISM": "Mouse"
},
"ChIPseq":{
"BLACKLISTBWAINDEX":"/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes/mm10.blacklist.chrM.chr_rDNA",
"BWA": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes/mm10",
"BOWTIE2INDEX": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes/mm10",
"CHROMS": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10",
"chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19",
"chrX","chrY","chrM"],
"EFFECTIVEGENOMESIZE": "2400000000", ### based upon Deeptools khmer output for 75bp fragments and rounded
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
"FASTAWITHADAPTERSETD": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.consolidated.fa",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/geneinfo.bed",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/ref.fa",
"GENOMECHR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/Chromsomes/",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/genes.gtf",
"KRAKENBACDB": "/fdb/kraken/20170202_bacteria",
"REFLEN":"/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes/mm10.fa.sizes",
},
}
}