Mini pheno repository

Data provided

This example phenotype data repository contains the following data:

• Two instruments files with a total of five measures
• Pedigree with six quad families
• Two measure description files (one has alternative data for demonstration purposes)
• A GPF instance directory with a configuration file

Additionally, there is a full copy of the data in an example input dir (example_input_dir). This copy is used to demonstrate the input_dir field in import configurations.

Import configs provided

• pheno_import_project_DEFAULT.yaml This is the default example import project. It uses the default input dir settings, which is to treat all paths in the import config relative to the directory it is located in. A basic override of instrument configuration is shown by using a different delimiter for the second instrument.

• pheno_import_project_INPUTDIR.yaml This import project is nearly identical to the default one, with the exception of manually setting the input_dir from which all other paths are considered relative to.

• pheno_import_project_NONSTANDARD_DESCRIPTIONS.yaml This import project demonstrates various overrides in specifying data dictionaries (files to read measure descriptions from), as well as manual input of measure descriptions inside the project.

Running the import

The commands below all produce their output into a directory called work.

import_phenotypes pheno_import_project_DEFAULT.yaml

import_phenotypes pheno_import_project_INPUTDIR.yaml

import_phenotypes pheno_import_project_NONSTANDARD_DESCRIPTIONS.yaml

Building a phenotype browser DB

To build a phenotype browser DB, you need to follow these steps:

1. Run any import of your choice
2. Run the following command:

   build_pheno_browser mini_pheno --gpf-instance minimal_pheno_instance/gpf_instance.yaml --no-cache -j 1

3. minimal_pheno_instance/cache/pheno/mini_pheno should now contain a phenotype browser database file.