Annotate SNPSift Files

The script annotate_snpsift.py can be used to match variants from input files to an instance of GraphKB. Copy the script locally and install the package dependencies.

Must use Python3.6 or higher

pip3 install graphkb pandas

Then the annotator can be run as follows

python annotate_snpsift.py <INPUT FILES> --output graphkb_annotations.tsv

By default this will use the pori-demo version of GraphKB which has a limited amount of data. This demo version is intended for demonstration/testing only and a custom or shared production instance of the GraphKB API. This can be configured via the GraphKB arguments. See the help menu for a full list of arguments.

python annotate_snpsift.py -h

The output file will contain the variant name and the annotations pulled from GraphKB.