Kids First Pedigree Builder

👪 Tools (and a python package supporting those tools) to allow querying Kids First data and building dbGaP-style pedigree files. Allows querying the open-access Kids First FHIR server, as well as the backend Kids First Dataservice and PostgreSQL database.

NOTE: Currently, this tool queries data that is only accessible from within the Kids First DRC. If you would like a pedigree file generated for you, please contact our support.

How to Install

To generate pedigree reports, clone this repo:

git clone https://github.com/kids-first/kf-utils-python.git

How to Use

n.b. ./pedigree_report build_pedi_report --help to see detailed usage of flags and options.

To generate a pedigree file for a study using the Kids First PostgreSQL database:

./pedigree_report build_pedi_report \
    --study_id SD_ME0WME0W \
    --db_url $DATABASE_URL \
    --output_file my_pedigree_file.txt

To generate a pedigree file for mulitple studies using the Kids First PostgreSQL database:

./pedigree_report build_pedi_report \
    -s SD_ME0WME0W -s SD_12345678 \
    --db_url $DATABASE_URL \
    --output_file my_pedigree_file.txt

To generate an additional participant-level metadata file, use the -m flag:

./pedigree_report build_pedi_report \
    --study_id SD_ME0WME0W \
    --db_url $DATABASE_URL \
    --output_file my_pedigree_file.txt \
    -m