config_laptop.yaml 1.22 KB
Newer Older
Beatrice Tan's avatar
Merged.  
Beatrice Tan committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
#Directories to be specified
#workdir: /home/bftan/CNA_results        #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2_test    #directory to install GISTIC2

#workdir: /home/bftan/CNA_results        #directory to write output
#gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2

workdir: /home/beatrice/CNA_analysis
gisticdir: /home/beatrice/CNA_analysis/run_gistic2

#Input details to download from firehose
cancer_type: SKCM
date_data: "2016_07_15"

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

#Data for running and benchmarking tools.
reference: hg19
prev_found_genes: input_files/intogen-CM-drivers-data.tsv
census_genes: input_files/Census_genes.txt
biomart_genes: input_files/biomart_human_genes.tsv

#Settings GISTIC2.0
gistic_precision: "99"
settings_gistic: "-ta 0.1
                  -td 0.1
                  -qvt 0.25
                  -brlen 0.7
                  -cap 1.5
                  -rx 1
                  -genegistic 1
                  -conf 0.99"

#Settings for sample size differences
sizes: [20, 30, 40, 50, 60, 70, 80, 90]
#sizes: [30, 40]
repeats: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]