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mm9.json
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mm9.json
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{
"references": {
"exomeseq": {
"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_known_snps.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",
"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",
"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",
"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": ""
},
"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/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",
"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",
"ALVIEWGENOME": "mm10",
"AVIASET": "mm10",
"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",
"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
"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": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/ref.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/genes.gtf",
"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/STAR/2.7.0f/genes-",
"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/qualimap_info.txt",
"KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/karyoplot_gene_coordinates.txt",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/annotate.genes.txt",
"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/annotate.isoforms.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/refFlat.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/genes.ref.bed",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/geneinfo.bed",
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/mm9.M1/",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/rsemref/mm9",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/mm9.rRNA_interval_list",
},
"rnaseqvargerm": {
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"GENOMEFILE": "/fdb/STAR_2.4.2a/GENCODE/Gencode_mouse/release_M4/ref.fa",
"GTFFILE": "/fdb/STAR_2.4.2a/UCSC/mm10/genes.gtf",
"STARDIR": "/fdb/STAR_2.4.2a/GENCODE/Gencode_mouse/release_M4/genes-",
"STARREF": "/fdb/STAR_2.4.2a/UCSC/mm10/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/Mm10.rRNA.interval_list_v3",
"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_known_snps.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",
"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",
"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",
"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": ""
},
"ChIPseq":{
"BWA": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/indexes/mm9",
"BOWTIE2INDEX": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/indexes/mm9",
"BLACKLISTBWAINDEX":"/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/indexes/mm9.blacklist.chrM.chr_rDNA",
"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",
"FASTQ_SCREEN_CONFIG2": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen_2.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/mm9_basic/geneinfo.bed",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/ref.fa",
"GENOMECHR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/Chromsomes/",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/genes.gtf",
"KRAKENBACDB": "/fdb/kraken/20170202_bacteria",
"REFLEN":"/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/indexes/mm9.fa.sizes",
},
}
}