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mm10.json~
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mm10.json~
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{"references": {
"exomeseq": {
"BWAGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa",
"GENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
<<<<<<< HEAD
"CHROMS": "/data/CCBR/db/PipeDB/lib/mm10_chromosomes",
"INDELSITES": "/data/CCBR/db/PipeDB/lib/sorted.dict.repaired_mgp.v5.merged.indels.dbSNP142.normed.vcf",
"NOVOINDEX": "/data/CCBR/db/PipeDB/lib/mm10_genome.nix",
"SNPSITES": "/data/CCBR/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",
=======
"ALVIEWGENOME": "mm10",
"CHROMS": "/data/CCBR/local/lib/mm10_chromosomes",
"INDELSITES": "/data/CCBR/local/lib/sorted.dict.repaired_mgp.v5.merged.indels.dbSNP142.normed.vcf",
"NOVOINDEX": "/data/CCBR/local/lib/mm10_genome.nix",
"SNPSITES": "/data/CCBR/local/lib/mm10_allstrains_dbSNP142.vcf",
>>>>>>> upstream/master
"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",
"ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
"ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
"nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
"nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
"ORGANISM": "MOUSE",
"SNP138": "/data/CCBR/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",
"REFFLAT": "/data/CCBR/db/PipeDB/lib/SS_mouse_exome_mm10_reformat.bed",
"SNPEFF_CONFIG": "/usr/db/PipeDB/apps/snpEff/4.2/snpEff.config",
"SNPEFF_GENOME": "GRCm38.82",
"FILTERSIFT": "( QUAL >= 20 )",
"MUTECTGENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
"MUTECTVARIANTS": "--dbsnp /data/CCBR/db/PipeDB/lib/mm10_allstrains_dbSNP142.vcf",
"STRELKA_CONFIG": "/data/CCBR/db/PipeDB/lib/strelka_demo_config.ini",
"DELLY_EXCLUSIONS": "/data/CCBR/db/PipeDB/lib/delly.mouse.mm10.excl.tsv",
"CNVKIT_TARGETS": "/data/CCBR/db/PipeDB/lib/mm10_cnvkit_targets_split.bed",
"FASTQ_SCREEN_CONFIG": "/data/CCBR/db/PipeDB/lib/fastq_screen.conf",
#below here is junk placeholders
"HAPMAP_DBNSFP": "/data/CCBR/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/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/dev/RNA-Seq-pipeline/ver3/Mm10_genes.txt",
"REFFLAT": "/data/CCBR/dev/RNA-Seq-pipeline/ver3/refFlatMm10.txt",
"RSEMREF": "/data/CCBR/dev/RNA-Seq-pipeline/ver3/rsemref/mouse_gencode",
"SALMONREF": "/data/CCBR/dev/RNA-Seq-pipeline/ver3/rsemref/mouse_gencode.transcripts.fa",
"FASTAWITHADAPTERSETC": "/data/CCBR/dev/RNA-Seq-pipeline/ver2/TruSeq_and_nextera_adapters_new.fa",
"RRNALIST": "/data/CCBR/dev/RNA-Seq-pipeline/ver3/Mm10.rRNA.interval_list_v3"
},
}
}