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Annotate Variant List

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

This example script expects a file with a single field (variant) and no header. Each line should be a separate HGVS-like variant notation. For example


Must use Python3.6 or higher

pip3 install graphkb pandas

Then the annotator can be run as follows

python <INPUT FILE> --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 -h

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

The names of the variants matched will be included in the output file as "variant_matches", this will be a semi-colon delimited list of all the variants which were considered to be present/equivalent based on the input variant. For example if the input where KRAS:p.G12D we might expect to see something like this

KRAS mutation;KRAS:p.(G12_G13)mut;KRAS:p.?12mut;KRAS:p.G12;KRAS:p.G12D;KRAS:p.G12mut;chr12:g.25398284C>T

We can see the variant has matched less specific forms of the same variant such as KRAS mutation or KRAS:p.(G12_G13)mut (any KRAS mutation at G12 or G13)

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