Tool for analysis of copy number profile in WGS.
git clone https://github.com/stjude/doCNA.git
# setup a virtual environment
python -m venv docna_install
source ./docna_install/bin/activate
# install into virtual environment
pip3 install ./doCNA# hg19 example
wget https://sandbox.zenodo.org/record/1181478/files/hg19_cytoBand.dat && echo 4036fc07b0b87ef28b46b1229141abb1 hg19_cytoBand.dat | md5sum --check
...
hg19_cytoBand.dat: OK
wget https://sandbox.zenodo.org/record/1181478/files/hg19_SuperGood.dat.gz && echo 8e3058f18c502a91b466d779a59a35f0 hg19_SuperGood.dat.gz | md5sum --check
...
hg19_SuperGood.dat.gz: OK
# hg38 example
wget https://sandbox.zenodo.org/record/1181478/files/hg38_cytoBand.dat && echo 5c957c934461320fdf6211df3d68bdd3 hg38_cytoBand.dat | md5sum --check
...
hg38_cytoBand.dat: OK
wget https://sandbox.zenodo.org/record/1181478/files/hg38_SuperGood.dat.gz && echo 1c32772977772ee1bab65f4be3a7acf2 hg38_SuperGood.dat.gz | md5sum --check
...
hg38_SuperGood.dat.gz: OK
- Get a local copy of the config:
docna getconfig-
Edit the config to point to real SuperGood and CytoBand files. We don't recommend changing additional parameters when starting out.
-
Run doCNA to generate output files:
# replace sample with whatever your samplename is
docna analyze -i Sample.txt -c doCNA.ini -s Sample
... Lots of log info! ...
12:18:19 doCNA.WGS: INFO: Ready to report!
All done- Launch the viewer and visualize output:
# if you are running this on your local machine, such as a desktop or laptop:
docna viewer
# if you are running this on a remote machine, like a cluster:
docna viewer --remote
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Access dashboard in browser via: http://10.220.16.129:39738
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INFO: Started server process [11716]
INFO: Waiting for application startup.
INFO: Application startup complete.
INFO: Uvicorn running on http://10.220.16.129:39738 (Press CTRL+C to quit)- Load files:
