Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Beatrice Tan
CNAprioritization
Commits
cc4e5d19
Commit
cc4e5d19
authored
Feb 03, 2018
by
Beatrice Tan
Browse files
Merged.
parent
90670433
Changes
1
Hide whitespace changes
Inline
Side-by-side
config_laptop.yaml
0 → 100644
View file @
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]
repeats
:
[
1
,
2
,
3
,
4
,
5
,
6
,
7
,
8
,
9
,
10
,
11
,
12
,
13
,
14
,
15
,
16
,
17
,
18
,
19
,
20
]
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment