1. Overview
We supply this Code Book to help researchers use aggV2 in their analysis. This is a live document and will be updated with new user feedback and requests.
The code snippets assume that you are working in the HPC environment and that you submit jobs to the cluster. Please see In-Depth Guide to HPC Usage for more information.
Feedback and Requests
For any feedback and requests to the aggV2 Code Book, or if you encounter issues running one of the examples, please reach out via the Genomics England Service Desk including "aggV2" in the title/description of your inquiry.
2. Applications
The majority of queries to aggV2 can be implemented using the applications below:
| Application | Description |
|---|---|
A set of utilities that manipulate variant calls in the Variant Call Format (VCF). Use version 1.10.2-foss-2018b via module load bio/BCFtools/1.10.2-foss-2018b | |
| split-vep | A bcftools plug-in to parse VEP annotation (comes with bcftools version 1.10.2-foss-2018b). |
| The LabKey client libraries (APIs) provide programmatic access to the clinical/phenotype data. | |
| For downstream processing. | |
| bedtools | To intersect, merge, count, complement, and shuffle genomic intervals. Use version 1.10.2-foss-2018b via |
We strongly recommend reading the above links to documentation on the respective tools.
3. Code book Structure
We have divided the Code Book into the following sections:
- aggV2 Code Book::General Information
- aggV2 Code Book::Genotype Queries
- aggV2 Code Book::Functional Annotation Queries
- aggV2 Code Book::Phenotype Queries
- aggV2 Code Book::Combining Queries