Downloading data
Downloading GENIE data
The GENIE data need to be downloaded from Synapse.
It is recommended to use the command line tool synapse
for downloading the
data. If you haven't done yet, install the synapseclient
Python package.
And then download the GENIE data into your current directory, here for version 15.0 of GENIE. Make sure you have registered for Synapse GENIE downloads and created a download token for Synapse, you will need it for authentication.
WARNING: Fixing the PROV-TRISEQ-V2 panel required.
There is an open issue with the PROV-TRISEQ-V2 panel, please see the
discussion on GENIE Synapse. To
fix this issue, the script fix_gene_panels.py
needs to be run once before using the genie
package. This script will add
a missing file for this panel in the gene_panels
directory of the GENIE
data.
You have to edit the line genie_dir
before calling fix_gene_panels.py
.
Downloading MANE transcript definitions
Download the latest release of MANE_\human from NCBI to the same directory where the genie data is stored. This is required for reannotating variants with MANE transcripts and for filtering for MANE transcripts.
download_mane.sh
Don't forget to update default_config.json
The file name of the MANE definition file is configured in
default_config.json
in the genie
GitHub repository. If you download a
new release of MANE, the filename in the config file needs to be updated.