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view test-data/varcalling.outdir/mutation_inspector.json @ 0:d4a8f440a518 draft

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Adding ctat_mutations tool.
author trinity_ctat
date Tue, 30 Oct 2018 12:28:26 -0400
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{
  "BAM": "/broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam", 
  "BAM_INDEX": "/broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bai", 
  "BED": "/seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/refGene.sort.bed", 
  "BED_INDEX": "/seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/refGene.sort.bed.idx", 
  "SAMPLE": "varcalling.outdir", 
  "SNV": [
    {
      "ALT": "G", 
      "CHASM_FDR": "0.2", 
      "CHASM_PVALUE": "0.1114", 
      "CHROM": "chr5", 
      "COSMIC_ID": "COSM4006021", 
      "DP": "4", 
      "GENE": "LOC100288152,SLC9A3", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "474989", 
      "QUAL": "96.03", 
      "REF": "A", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "urinary_tract", 
      "TUMOR": "carcinoma_--_NS", 
      "VEST_FDR": "1", 
      "VEST_PVALUE": "0.96802"
    }, 
    {
      "ALT": "A", 
      "CHASM_FDR": "0.15", 
      "CHASM_PVALUE": "0.0694", 
      "CHROM": "chr5", 
      "COSMIC_ID": "NA", 
      "DP": "45", 
      "GENE": "TRIM41", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "181224474", 
      "QUAL": "349.77", 
      "REF": "G", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "NA", 
      "TUMOR": "NA", 
      "VEST_FDR": "1", 
      "VEST_PVALUE": "0.48052"
    }, 
    {
      "ALT": "A", 
      "CHASM_FDR": "0.1", 
      "CHASM_PVALUE": "0.0344", 
      "CHROM": "chr8", 
      "COSMIC_ID": "COSM3750086", 
      "DP": "66", 
      "GENE": "PLEC", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "143923759", 
      "QUAL": "838.77", 
      "REF": "G", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "large_intestine", 
      "TUMOR": "carcinoma_--_adenocarcinoma", 
      "VEST_FDR": "1", 
      "VEST_PVALUE": "0.84202"
    }, 
    {
      "ALT": "A", 
      "CHASM_FDR": "0.15", 
      "CHASM_PVALUE": "0.0744", 
      "CHROM": "chr12", 
      "COSMIC_ID": "COSM3753397", 
      "DP": "48", 
      "GENE": "TIMELESS", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "56420869", 
      "QUAL": "384.77", 
      "REF": "G", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "large_intestine", 
      "TUMOR": "carcinoma_--_adenocarcinoma", 
      "VEST_FDR": "0.95", 
      "VEST_PVALUE": "0.18439"
    }, 
    {
      "ALT": "T", 
      "CHASM_FDR": "0.05", 
      "CHASM_PVALUE": "0", 
      "CHROM": "chr17", 
      "COSMIC_ID": "COSM3717625", 
      "DP": "61", 
      "GENE": "TP53", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "7673767", 
      "QUAL": "1848.77", 
      "REF": "C", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "bone", 
      "TUMOR": "Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS", 
      "VEST_FDR": "0.15", 
      "VEST_PVALUE": "0.01447"
    }, 
    {
      "ALT": "C", 
      "CHASM_FDR": "0.15", 
      "CHASM_PVALUE": "0.087", 
      "CHROM": "chr17", 
      "COSMIC_ID": "COSM3766193", 
      "DP": "80", 
      "GENE": "TP53", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "7676154", 
      "QUAL": "2161.77", 
      "REF": "G", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "haematopoietic_and_lymphoid_tissue", 
      "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia", 
      "VEST_FDR": "1", 
      "VEST_PVALUE": "0.52717"
    }, 
    {
      "ALT": "C", 
      "CHASM_FDR": "0.1", 
      "CHASM_PVALUE": "0.0372", 
      "CHROM": "chr17", 
      "COSMIC_ID": "COSM3755560", 
      "DP": "4", 
      "GENE": "BRCA1", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "43071077", 
      "QUAL": "92.03", 
      "REF": "T", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "haematopoietic_and_lymphoid_tissue", 
      "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia", 
      "VEST_FDR": "1", 
      "VEST_PVALUE": "0.3446"
    }, 
    {
      "ALT": "C", 
      "CHASM_FDR": "0.05", 
      "CHASM_PVALUE": "0.0002", 
      "CHROM": "chr17", 
      "COSMIC_ID": "COSM3755561", 
      "DP": "4", 
      "GENE": "BRCA1", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "43091983", 
      "QUAL": "84.03", 
      "REF": "T", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "soft_tissue", 
      "TUMOR": "haemangioblastoma_--_NS", 
      "VEST_FDR": "1", 
      "VEST_PVALUE": "0.64447"
    }, 
    {
      "ALT": "A", 
      "CHASM_FDR": "0.05", 
      "CHASM_PVALUE": "0.0004", 
      "CHROM": "chr17", 
      "COSMIC_ID": "COSM3755564", 
      "DP": "2", 
      "GENE": "BRCA1", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "43092919", 
      "QUAL": "33.74", 
      "REF": "G", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "prostate", 
      "TUMOR": "carcinoma_--_NS", 
      "VEST_FDR": "1", 
      "VEST_PVALUE": "0.33539"
    }, 
    {
      "ALT": "T", 
      "CHASM_FDR": "0.05", 
      "CHASM_PVALUE": "0.0014", 
      "CHROM": "chr17", 
      "COSMIC_ID": "COSM4989394", 
      "DP": "11", 
      "GENE": "BRCA1", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "43093454", 
      "QUAL": "425.77", 
      "REF": "C", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "soft_tissue", 
      "TUMOR": "rhabdomyosarcoma_--_embryonal", 
      "VEST_FDR": "1", 
      "VEST_PVALUE": "0.51068"
    }, 
    {
      "ALT": "C", 
      "CHASM_FDR": "0.05", 
      "CHASM_PVALUE": "0.0004", 
      "CHROM": "chr19", 
      "COSMIC_ID": "NA", 
      "DP": "106", 
      "GENE": "PAK4", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "39177761", 
      "QUAL": "1134.77", 
      "REF": "G", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "NA", 
      "TUMOR": "NA", 
      "VEST_FDR": "0.15", 
      "VEST_PVALUE": "0.01093"
    }, 
    {
      "ALT": "C", 
      "CHASM_FDR": "0.15", 
      "CHASM_PVALUE": "0.093", 
      "CHROM": "chr19", 
      "COSMIC_ID": "COSM3721172", 
      "DP": "12", 
      "GENE": "CCDC9", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "47271515", 
      "QUAL": "336.77", 
      "REF": "T", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "haematopoietic_and_lymphoid_tissue", 
      "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia", 
      "VEST_FDR": "1", 
      "VEST_PVALUE": "0.97622"
    }, 
    {
      "ALT": "T", 
      "CHASM_FDR": "0.15", 
      "CHASM_PVALUE": "0.0834", 
      "CHROM": "chr20", 
      "COSMIC_ID": "COSM3758608", 
      "DP": "26", 
      "GENE": "TP53RK", 
      "KGPROD": "NA", 
      "MQ": "60", 
      "NSF": "NA", 
      "NSM": "NA", 
      "NSN": "NA", 
      "PMC": "NA", 
      "POS": "46687147", 
      "QUAL": "423.77", 
      "REF": "C", 
      "RS": "NA", 
      "SAO": "NA", 
      "TISSUE": "pancreas", 
      "TUMOR": "carcinoma_--_ductal_carcinoma", 
      "VEST_FDR": "1", 
      "VEST_PVALUE": "0.88584"
    }
  ]
}