This module provides a drush command to load genotypic data from a variety of file formats including Variant Call Format (VCF), Genotype Matrix and Genotype Flat-File formats as described below. It stores genotype calls in the custom chado-esque genotype_call table; whereas, all other meta data is stored in a chado-compliant manner.
- Tripal 3.x (Installation Instructions)
- PostgreSQL 9.3 (9.4+ recommended; tested with 11.3)
This module is installed by cloning it and it's dependencies in [your drupal site]/sites/all/modules and enabling it through the Drupal Administrative UI. Specifically, once you have a working Tripal environment:
cd [drupal root]/sites/all/modules
git clone https://github.com/uofs-pulse-binfo/genotypes_loader
drush pm-enable genotypes_loader
- Extensive configuration allowing for flexiblity in ontology terms used.
- Drush command for easy import of VCF, genotypes matrix and flatfile formats.
- Both prompt and option support for drush command, making it easy for scripting, as well as, human interaction.
- genotype_call table for efficient data storage.
Please visit our online documentation to learn more about installation, usage and features.
If you would like to evaluate this module using demonstration data, there is a full tutorial in our documentation.
This work is supported by Saskatchewan Pulse Growers [grant: BRE1516, BRE0601], Western Grains Research Foundation, Genome Canada [grant: 8302, 16302], Government of Saskatchewan [grant: 20150331], and the University of Saskatchewan.
Caron, C. and Sanderson, L.A. (2020). Genotypes Loader: Efficient large-scale genotypic data import into Chado. Version 1.0. University of Saskatchewan, Pulse Crop Research Group, Saskatoon, SK, Canada.