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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: 

ApplicationDescription

bcftools

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-vepA bcftools plug-in to parse VEP annotation (comes with bcftools version 1.10.2-foss-2018b). 

LabKey APIs

The LabKey client libraries (APIs) provide programmatic access to the clinical/phenotype data. 

R / Python

For downstream processing. 
bedtools

To intersect, merge, count, complement, and shuffle genomic intervals. Use version 1.10.2-foss-2018b via module load bio/BEDTools/2.27.1-foss-2018b

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: