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CNAprioritization
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Beatrice Tan
CNAprioritization
Commits
cc4e5d19
Commit
cc4e5d19
authored
Feb 03, 2018
by
Beatrice Tan
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cc4e5d19
#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]
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