kamichiotti/mc3

mc3

The TCGA PanCancer Atlas MC3 set is a re-calling of uniform files to remove batch effects and enable pancancer analysis.

Example run:

Running MC3

Original Job list

https://www.synapse.org/#!Synapse:syn4977808

Obtain GDC download token

Obtain BAM files

../tools/gdc-download-tool/gdc-client download -t ../gdc.token fb0bed68-4f2c-400d-8460-a62310fa95bf

../tools/gdc-download-tool/gdc-client download -t ../gdc.token ded8b01f-5301-49c8-bfdc-fc8343291e6d

Example Variant Calling input

{
    "tumor" : {
      "class" : "File",
      "path" : "/mnt/mc3/mc3/seq/ded8b01f-5301-49c8-bfdc-fc8343291e6d/C317.TCGA-AB-2901-03A-01W-0733-08.4.bam"
    },
    "normal" : {
      "class" : "File",
       "path" : "/mnt/mc3/mc3/seq/fb0bed68-4f2c-400d-8460-a62310fa95bf/C317.TCGA-AB-2901-11A-01W-0732-08.4.bam"
    },
    "centromere" : {
      "class" : "File",
      "path" : "/mnt/mc3/mc3/vcfs//centromere_hg19.bed"
    },
    "cosmic" : {
      "class" : "File",
        "path" : "/mnt/mc3/mc3/ref/b37_cosmic_v54_120711.vcf.gz"
    },
    "dbsnp" : {
        "class" : "File",
        "path" : "/mnt/mc3/mc3/ref/dbsnp_132_b37.leftAligned.vcf.gz"
    },
    "reference" : {
        "class" : "File",
        "path"  :  "/mnt/mc3/mc3/ref/Homo_sapiens_assembly19.fasta.gz"
    },
    "bed_file" : {
        "class" : "File",
        "path" : "/mnt/mc3/mc3/vcfs/gaf_20111020+broad_wex_1.1_hg19.bed"
    },
    "tumor_analysis_uuid" : "cf8c9b38-246d-46aa-b557-6c882e438161",
    "tumor_aliquot_uuid" : "bac6a6d2-8c40-43cd-ab4c-16d3f8a06eb6",
    "normal_analysis_uuid" : "c404dcfb-e580-4cf2-8fe6-6990ce2ce03a",
    "normal_aliquot_uuid" : "22f3f166-41a7-4058-a315-d72e1d7becd6",
    "platform" : "illumina",
    "center" : "OHSU"
}

Example Vcf2Maf input

{
    "normalID" : "TCGA-AB-2901-11A-01W-0732-08",
    "tumorID" : "TCGA-AB-2901-03A-01W-0733-08",
   "museVCF" : {
     "class" : "File",
     "path" : "/mnt/mc3/mc3/test/C317.TCGA-AB-2901-03A-01W-0733-08.4.muse.tcga_filtered.reheadered.vcf"
   },
   "mutectVCF" : {
       "class" : "File",
       "path"  : "/mnt/mc3/mc3/vcfs/008ddf20-f7fb-4673-b2ed-b5d5212fbf09_TB_NT_bac6a6d2-8c40-43cd-ab4c-16d3f8a06eb6_22f3f166-41a7-4058-a315-d72e1d7becd6.oxoG.snp.capture.tcga.vcf",
   },
    "indelocatorVCF" : {
       "class" : "File",
       "path" : "/mnt/mc3/mc3/vcfs/008ddf20-f7fb-4673-b2ed-b5d5212fbf09_TB_NT_bac6a6d2-8c40-43cd-ab4c-16d3f8a06eb6_22f3f166-41a7-4058-a315-d72e1d7becd6.indel.capture.tcga.vcf"
    },
   "somaticsniperVCF" : {
       "class" : "File",
       "path" : "/mnt/mc3/mc3/test/C317.TCGA-AB-2901-03A-01W-0733-08.4.SomaticSniper.annotated.tcga_filtered.reheadered.vcf"
   },
   "varscansVCF" : {
       "class" : "File",
       "path" : "/mnt/mc3/mc3/test/C317.TCGA-AB-2901-03A-01W-0733-08.4.varscan.snp.annotated.tcga_filtered.reheadered.vcf",
   },
   "varscaniVCF" : {
       "class" : "File",
       "path" : "/mnt/mc3/mc3/test/C317.TCGA-AB-2901-03A-01W-0733-08.4.varscan.indel.annotated.tcga_filtered.reheadered.vcf"
   },
   "radiaVCF" : {
       "class" : "File",
       "path" : "/mnt/mc3/mc3/test/filtered.radia.tcga_filtered.reheadered.vcf"
   },
   "pindelVCF" : {
       "class" : "File",
       "path" : "/mnt/mc3/mc3/test/C317.TCGA-AB-2901-03A-01W-0733-08.4.pindel.somatic.tcga_filtered.reheadered.vcf"
   },
   "indelocatorVCF" : {
       "class" : "File",
       "path" : "/mnt/mc3/mc3/test/indelocator_filtered.reheadered.vcf"
   },
   "vepData" : {
       "class" : "Directory",
       "path" : "/mnt/mc3/mc3/vep-data"
   },
   "refFasta" : {
     "class" : "File",
     "path" : "Homo_sapiens_assembly19.fasta.gz"
   }
}