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hg38.json
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hg38.json
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{"references": {
"exomeseq": {
"VARDICTBED": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.chroms.bed",
"BWAGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.noCOSMIC_ClinVar.pon.vcf.gz",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
# "CNVKITREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1_flatRef.cnn",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch38.bed",
"INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
# "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_g1k_v37_iupac.nix",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/reformatS04380219_qualimap.bed",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
# "KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
"KNOWNVCF2": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"SNPSITES": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_146.hg38.vcf.gz",
"KNOWNINDELS": "-known /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -known /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz -knownSites /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_theta_SNPfile.txt",
"INDELSITES2": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"ALVIEWGENOME": "hg38",
"CONPAIRMARKERSA": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt",
"CONPAIRMARKERSB": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_exons.bed",
# "ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
"STRELKA_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/strelka_demo_config.ini",
"CNVKIT_TARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_SSv5_cnvkit_targets.bed",
"CNVKIT_ANTITARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_SSv5_cnvkit_antitargets.bed",
"DELLY_EXCLUSIONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/delly.human.hg38.excl.tsv",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"tg_PHASE_INDELS": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"SNP138": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"HAPMAP": "/fdb/GATK_resource_bundle/hg38bundle/hapmap_3.3.hg38.vcf.gz",
"B1K": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"OMNI": "/fdb/GATK_resource_bundle/hg38bundle/1000G_omni2.5.hg38.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",
"ORGANISM": "HUMAN",
"AVIASET": "hg38",
"ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
"ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
"nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
"nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
# "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
# "FILTERSIFT": "(FILTER='PASS') & ( QUAL >= 20 )", ###maybe change to 30
# "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": "GRCh38.86",
"HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
"REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
"MUTECTCOSMIC": "/data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
"MUTECTSNP": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"MUTECTGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"MUTECTVARIANTS": "--dbsnp /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz --cosmic /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
"VEPBUILD": "GRCh38",
"VEPSPECIES": "homo_sapiens",
"VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/ExAC_nonTCGA.r0.3.1.sites.vep.GRCh38.vcf.gz",
"VEPGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"CANVASGENOME": "/fdb/Canvas/GRCh38/WholeGenomeFasta",
"CANVASKMER": "/fdb/Canvas/GRCh38/kmer.fa",
"CANVASFILTER": "/fdb/Canvas/GRCh38/filter13.bed",
"CANVASPLOIDY": "/data/CCBR_Pipeliner/db/PipeDB/lib/ploidy.vcf",
"CANVASBALLELES": "/fdb/Canvas/GRCh38/dbsnp.vcf",
"CNVKITANNO": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_refFlat.txt",
"FREECLENGTHS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.filtered.fa.fai",
"FREECCHROMS": "/fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/Chromosomes",
"FREECFASTA": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"FREECPILEUP": "/data/CCBR_Pipeliner/db/PipeDB/lib/dbsnp_146.hg38.SingleDiNucl.IDs.vcf",
"FREECSNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/dbsnp_146.hg38.SingleDiNucl.IDs.vcf",
"SEQUENZAGC": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_gc50Base.txt.gz",
},
"genomeseq": {
"VARDICTBED": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.chroms.bed",
"BWAGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.noCOSMIC_ClinVar.pon.vcf.gz",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"CNVKITREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1_flatRef.cnn",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch38.bed",
"CNVKITWGSTARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_cnvkit_wgs_targets.bed",
"CNVKITANTITARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/fake.antitargetcoverage.cnn",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
"CNVKITANNO": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_refFlat.txt",
"INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
# "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_g1k_v37_iupac.nix",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/reformatS04380219_qualimap.bed",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
# "KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
"KNOWNVCF2": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"SNPSITES": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_146.hg38.vcf.gz",
"KNOWNINDELS": "-known /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -known /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz -knownSites /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_theta_SNPfile.txt",
"INDELSITES2": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"ALVIEWGENOME": "hg38",
"CONPAIRMARKERSA": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt",
"CONPAIRMARKERSB": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_exons.bed",
# "ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
"STRELKA_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/strelka_demo_config.ini",
"DELLY_EXCLUSIONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/delly.human.hg38.excl.tsv",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"tg_PHASE_INDELS": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"SNP138": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"HAPMAP": "/fdb/GATK_resource_bundle/hg38bundle/hapmap_3.3.hg38.vcf.gz",
"B1K": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"OMNI": "/fdb/GATK_resource_bundle/hg38bundle/1000G_omni2.5.hg38.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",
"ORGANISM": "HUMAN",
"AVIASET": "hg38",
"ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
"ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
"nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
"nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
# "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
# "FILTERSIFT": "(FILTER='PASS') & ( QUAL >= 20 )", ###maybe change to 30
# "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": "GRCh38.86",
"HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
"REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
"MUTECTCOSMIC": "/data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
"MUTECTSNP": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"MUTECTGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"MUTECTVARIANTS": "--dbsnp /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz --cosmic /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
"VEPBUILD": "GRCh38",
"VEPSPECIES": "homo_sapiens",
"VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/ExAC_nonTCGA.r0.3.1.sites.vep.GRCh38.vcf.gz",
"VEPGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"CANVASGENOME": "/fdb/Canvas/GRCh38/WholeGenomeFasta",
"CANVASKMER": "/fdb/Canvas/GRCh38/kmer.fa",
"CANVASFILTER": "/fdb/Canvas/GRCh38/filter13.bed",
"CANVASPLOIDY": "/data/CCBR_Pipeliner/db/PipeDB/lib/ploidy.vcf",
"CANVASBALLELES": "/fdb/Canvas/GRCh38/dbsnp.vcf",
"CNVKITANNO": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_refFlat.txt",
"FREECLENGTHS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.filtered.fa.fai",
"FREECCHROMS": "/fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/Chromosomes",
"FREECFASTA": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"FREECPILEUP": "/data/CCBR_Pipeliner/db/PipeDB/lib/dbsnp_146.hg38.SingleDiNucl.IDs.vcf",
"FREECSNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/dbsnp_146.hg38.SingleDiNucl.IDs.vcf",
"SEQUENZAGC": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_gc50Base.txt.gz",
},
"rnaseq": {
"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/ref.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/genes.gtf",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/annotate.genes.txt",
"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/annotate.isoforms.txt",
"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/qualimap_info.txt",
"KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/karyoplot_gene_coordinates.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/refFlat.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/genes.ref.bed",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/geneinfo.bed",
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/hg.v26/",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/rsemref/hg38",
"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/STAR/2.7.0f/genes-",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/hg38.rRNA_interval_list",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"FUSIONGTFFILE": "/fdb/GENCODE/Gencode_human/release_26/gencode.v26.annotation.gtf",
# "REFFLAT2": "/data/CCBR_Pipeliner/db/PipeDB/dev/refFlatHg38_R26.txt",
# "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/hg38_R26/human_gencode.transcripts.fa",
# "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/dev/RNA-Seq-pipeline/ver2/TruSeq_and_nextera_adapters_new.fa",
"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
"STARREF": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_human/release_26/genes-",
# "RRNALIST2": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38.rRNA.interval_list_R26",
"STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38_gencode_v29_CTAT_lib_Mar272019.plug-n-play/ctat_genome_lib_build_dir",
"FUSCATCHDAT": "/usr/local/apps/fusioncatcher/1.10/fusioncatcher/data/human_v95",
"FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
"GENOME": "/fdb/GENCODE/Gencode_human/release_26/GRCh38.primary_assembly.genome.fa",
# "INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz",
"KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
"KNOWNVCF2": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"SNPSITES": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_146.hg38.vcf.gz",
"KNOWNINDELS": "-known /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -known /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz -knownSites /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
# "THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_theta_SNPfile.txt",
"INDELSITES2": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"ALVIEWGENOME": "hg38",
"ONCOFUSEBUILD": "hg38",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_exons.bed",
# "ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
# "tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
# "tg_PHASE_INDELS": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
# "SNP138": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
# "HAPMAP": "/fdb/GATK_resource_bundle/hg38bundle/hapmap_3.3.hg38.vcf.gz",
# "B1K": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
# "OMNI": "/fdb/GATK_resource_bundle/hg38bundle/1000G_omni2.5.hg38.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",
"ORGANISM": "HUMAN",
"AVIASET": "hg38",
# "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
# "ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
# "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
# "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
# "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
# "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": "GRCh38.86",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
# "HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
# "REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
},
"rnaseqvargerm": {
"GENOMEFILE": "/fdb/GENCODE/Gencode_human/release_19/GRCh37.p13.genome.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/lib/GENCODE_GRCh37_ref_annot.gtf",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg19_genes.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_GENCODE_GENE_V19_comprehensive.bed",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/human_gencode",
"SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/human_gencode.transcripts.fa",
"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
"STARDIR": "/fdb/STAR_2.4.2a/GENCODE/Gencode_human/release_19/genes-",
"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/Star_refs/hs37d5/genes-",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg19.rRNA.interval_list_v3",
# "BWAGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa",
"CHROMS": ["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y","MT"],
# "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa",
"CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch37.bed",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
"INDELSITES": "/fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf",
"NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_g1k_v37_iupac.nix",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/dev/refFlatHg19.txt",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.vcf.gz",
"KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
"KNOWNVCF2": "/fdb/GATK_resource_bundle/b37-2.8/1000G_phase3_v4_20130502.sites.vcf.gz",
"SNPSITES": "/fdb/GATK_resource_bundle/b37/dbsnp_138.b37.vcf",
"KNOWNINDELS": "-known /fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -known /fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
"KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/b37/dbsnp_138.b37.vcf -knownSites /fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -knownSites /fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
"THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_theta_SNPfile.txt",
"INDELSITES2": "/fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
"ALVIEWGENOME": "hg19",
"CONPAIRMARKERS": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19.exons.bed",
"ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
"STRELKA_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/strelka_demo_config.ini",
"CNVKIT_TARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_SSv5_cnvkit_targets.bed",
"CNVKIT_ANTITARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_SSv5_cnvkit_antitargets.bed",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch37.bed",
"DELLY_EXCLUSIONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/delly.human.hg19.excl.tsv",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"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_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",
"ORGANISM": "HUMAN",
"AVIASET": "hg19",
"ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
"ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
"nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
"nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
"gencodeGtf":"gencode.vM4.all.gtf",
"genomeRnaseq": "GRCm38.p3.genome.fa",
"genomeDir": "/data/CCBR_Pipeliner/db/PipeDB/lib/genomes",
"gtfDir": "/data/CCBR_Pipeliner/db/PipeDB/lib/gtf",
"genomeDir2": "/data/CCBR_Pipeliner/db/PipeDB/lib/genomes/2pass",
"gtfERCC": "gencode.vM4.all_ERCC.gtf",
"genomeRnaseqErcc": "GRCm38.p3.ERCC.genome.fa",
"DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
"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_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
"REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
"MUTECTCOSMIC": "/data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
"MUTECTSNP": "/fdb/muTect/dbsnp_137.b37.vcf",
"MUTECTGENOME": "/fdb/muTect/human_g1k_v37.fasta",
"MUTECTVARIANTS": "--dbsnp /fdb/muTect/dbsnp_137.b37.vcf --cosmic /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz"
},
"mirseq": {
"BOWTIE_REF": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/bowtie_indices/hg38",
"FASTA_REF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/hg38_basic.fa",
"MIRBASE_MATURE": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/miRBase_v22/hsa_mature.fa",
"MIRBASE_HAIRPIN": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/miRBase_v22/hsa_hairpin.fa",
"ORGANISM": "Human",
"run_info":{
"TOOL": "miRNA",
"VERSION": "1.1",
"PI": "NA",
"FLOWCELL": "external",
"GENOME_BUILD": "hg38",
"MIRBASE_VERSION": "21",
"EMAIL": "[email protected]",
# "SAMPLENAMES": "dA549-KD-a-1_S4_R1_001:dA549-NCTR-a-1_S1_R1_001:dA549-KO-a-2_S5_R1_001:dA549-NCTR-a-2_S3_R1_001:dA549-KD-b-1_S8_R1_001:dA549-NCTR-b-1_S6_R1_001:dA549-KD-b-2_S2_R1_001:dA549-NCTR-b-2-2_S2_R1_001:dH460-KOa-1_S3_R1_001:dH460-NCTR-a-1_S1_R1_001:dH460-KOa-2_S4_R1_001:dH460-NCTR-a-2_S2_R1_001:dH460-KO-b-1_S6_R1_001:dH460-NCTR-b-1_S5_R1_001:dH460-KO-b-2_S8_R1_001:dH460-NCTR-b-2-2_S1_R1_001",
# "LANEINDEX": "-:-:-:-",
"TRIM_ADAPTER": "YES",
"CALL_SNVS": "YES",
"DIFF_EXPRESSION": "YES",
"DIFF_EXPRESSION_ANALYSES": "mir_knockdown",
# "INPUT_DIR": "/",
# "OUTPUT_DIR": "out",
"TOOL_INFO": "tool_info",
"SAMPLE_INFO": "sample_info",
# "DELIVERY_FOLDER": "/scratch/dwheeler/test5/out",
# "USE_SGE": "0",
# "USE_PORTAL": "0",
# "PORTAL_PROJECT_NAME": "NA"
},
"reference_files": {
"BOWTIE_REF": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/genome",
"GENCODE_GTF": "/fdb/GENCODE/GRCh38/21/GTF/gencode.v21.annotation.gtf",
"MIRBASE_GFF": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/hsa.gff3",
"MIRBASE_HAIRPIN": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/hairpin.fa",
"MIRBASE_MATURE": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/mature.fa",
# For miRspring which uses its own set of files
"MIRBASE_FILES": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References",
# "MIRBASE_GFF": "/data/dwheeler/miRspring/miRbase_Files/hsa.gff2",
# "MIRBASE_HAIRPIN": "/data/dwheeler/miRspring/miRbase_Files/hsa.nt35.fa",
# "MIRBASE_MATURE": "/data/dwheeler/miRspring/miRbase_Files/mature.fa",
# "MIRBASE_FILES": "/data/dwheeler/miRspring/miRbase_Files/",
"REF_GENOME": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/genome.fa",
"REF_GENOME_IUPAC": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/genome-iupac.fa",
"TARGET_DATA": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References",
},
},
"ChIPseq":{
"BWA": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/indexes/hg38",
"BOWTIE2INDEX": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/indexes/hg38",
"BLACKLISTBWAINDEX":"/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/indexes/hg38.blacklist.chrM",
"CHROMS": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10",
"chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19",
"chr20","chr21","chr22","chrX","chrY","chrM"],
"EFFECTIVEGENOMESIZE": "2700000000", ### based upon Deeptools khmer output for 75bp fragments and rounded
"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",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/geneinfo.bed",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/ref.fa",
"GENOMECHR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/Chromsomes/",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/genes.gtf",
"KRAKENBACDB": "/fdb/kraken/20170202_bacteria",
"REFLEN":"/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/indexes/hg38.fa.sizes",
},
}
}