This is a forked version of verilylifesciences/variant-annotation. The intention is to gradually update various pieces of this repo for variant annotation needs we have in googlegenomics/gcp-variant-transforms but at the same time provide annotation related tools/documentation that:
- can be used independently,
- are actively maintained with proper test harnesses.
Any README file that has the following warning message indicates a sub-directory that has not been updated yet:
WARNING: Not actively maintained!
This is the list of modules that are actively maintained:
batch/vep
This repository contains code to annotate human sequence variants using cloud technology to perform analyses in parallel.
Sub-projects:
- batch annotation code for annotating a particular batch of variants using annotation resources available at a particular point in time
- interactive annotation queries and code to annotate variants interactively with new annotation resources as they become available
- annotation curation code for ingesting and reformating raw annotation resources for use in interactive annotation
The code in this repository is designed for use with genomic variants stored in Google BigQuery in a particular variant table format.
Processing uses Google Container Builder, Docker, and dsub for batch processing. We suggest working through the introductory materials for each tool before working with the code in this repository.
For interactive annotation, parallelism is accomplished due to the use of BigQuery. For batch annotation, parallelism is accomplished due to the use of dsub to run annotation in parallel on small shards of the input file(s).