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config_common.json
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config_common.json
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{
"pipeline_version" : "v3.0dev",
"mail" : "-c patidarr@mail.nih.gov",
"mails" : "-c patidarr@mail.nih.gov -c manoj.tyagi@nih.gov -c wangc@mail.nih.gov -c yujin.lee@nih.gov -c NCIBioinformatics_Oncogenomics@mail.nih.gov",
"platform" : "Illumina",
"samtools" : "0.1.19",
"samtools_old" : "0.1.19",
"fastqc" : "0.11.2",
"bedtools" : "2.22.0",
"bwa" : "0.7.10",
"bismark" : "0.17.0",
"STAR" : "2.4.0k",
"picard" : "1.129",
"bamutil" : "1.0.13",
"GATK" : "3.4-0",
"bam2mpg" : "1.0.1",
"MuTect" : "1.1.7",
"strelka" : "1.0.14",
"vcftools" : "0.1.13",
"platypus" : "0.8.1",
"freebayes" : "0.9.21",
"snpEff" : "4.1c",
"qualimap" : "2.1.3",
"annovar" : "2015-03-22",
"snpEff_genome" : "GRCh37.75",
"build" : "hg19",
"SIFT" : "5.2.2",
"SIFTbuild" : "Human_db_37",
"polyphen2" : "2.2.2r405b",
"novocraft" : "3.02.10mpich2",
"tophat" : "2.0.13",
"bowtie" : "1.1.1",
"igvtools" : "2.3.31",
"cufflinks" : "2.2.1_patched",
"fusioncatcher" : "0.99.5a",
"defuse" : "0.7.0",
"pypy" : "5.0",
"verifybamid" : "1.1.3",
"conpair" : "10102016",
"cnvkit" : "0.8.5",
"pvacseq" : "4.0.6",
"Actionable_mutation" : "Actionable.v3.pl",
"Actionable_fusion" : "ActionableFusion.v1.pl",
"Panel_List" : ["clin.snv.v1", "clin.cnv.v2", "clin.snv.v2", "nbl.panel", "seqcapez.rms.v1"],
"failed_exon_params": {
"wholegenome" :{"Normal":"5","Tumor":"5"},
"seqcapez.hu.ex.v3" :{"Normal":"20","Tumor":"20"},
"seqcapez.hu.ex.utr.v1" :{"Normal":"20","Tumor":"20"},
"clin.ex.v1" :{"Normal":"10","Tumor":"20"},
"clin.snv.v1" :{"Normal":"20","Tumor":"50"},
"clin.cnv.v2" :{"Normal":"20","Tumor":"20"},
"clin.snv.v2" :{"Normal":"20","Tumor":"50"},
"seqcapez.rms.v1" :{"Normal":"100","Tumor":"100"},
"nbl.panel" :{"Normal":"100","Tumor":"100"},
"Agilent.Exon50M" :{"Normal":"20","Tumor":"20"},
"agilent.utr.v4" :{"Normal":"20","Tumor":"20"},
"agilent.v4" :{"Normal":"20","Tumor":"20"},
"agilent.v5" :{"Normal":"20","Tumor":"20"},
"agilent.utr.v5" :{"Normal":"20","Tumor":"20"},
"niaid.agilent.v5" :{"Normal":"20","Tumor":"20"},
"niaid.seqcapez.exome.v2":{"Normal":"20","Tumor":"20"},
"niaid.truseq.exome" :{"Normal":"20","Tumor":"20"},
"nextera" :{"Normal":"20","Tumor":"20"},
"strexome" :{"Normal":"20","Tumor":"20"},
"sureselect.exon.v5_utr":{"Normal":"20","Tumor":"20"},
"sureselect.exon.v6" :{"Normal":"20","Tumor":"20"},
"mayo_v5_urt" :{"Normal":"20","Tumor":"20"},
"idt.xgen.exome.res" :{"Normal":"10","Tumor":"20"}
}
}