config.yaml 1.25 KB
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#Directories to be specified
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#workdir: /home/bftan/CNA_results        #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
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workdir: /exports/sasc/hmei/test_CNV        #directory to write output
gisticdir: /exports/sasc/hmei/GISTIC2    #directory to install GISTIC2
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#Input details to download from firehose
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cancer_type: SKCM
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date_data: "2016_07_15"

#Or provide input file
inputfile: ""   #tumor segmentation data
normal: ""      #normal segmentation data

#Data for running and benchmarking tools.
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reference: hg19
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prev_found_genes: input_files/intogen-CM-drivers-data.tsv
census_genes: input_files/Census_genes.txt
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biomart_genes: input_files/biomart_human_genes_hg19.tsv
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ID_to_GO: input_files/ID_to_GO.txt
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#Settings GISTIC2.0
gistic_precision: "99"
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settings_gistic: "-brlen 0.98 -genegistic 1"
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#GISTIC2.0 settings to compare
comparison_precision: ["99", "90", "75"]
comparison_settings: ["-brlen 0.7 -genegistic 1",
                      "-brlen 0.98 -genegistic 1",
                      "-brlen 0.98 -genegistic 0",
                      "-brlen 0.7 -genegistic 0"]
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#Settings for sample size differences
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sizes: [20, 30, 40, 50, 60, 70, 80, 90]
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repeats: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]