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Dave Lawrence edited this page Dec 7, 2023 · 30 revisions

Wiki

The wiki is for technical documentation. See also user guide

Table of Contents

Scope

VariantGrid aims to allow biologists and medical scientists to perform filtering, visualisation and curation of variant (ie VCF derived) data themselves via a graphical interface.

We aim to integrate with existing mapping & variant calling pipelines, LIMS and patient record systems in labs.

System Overview

  • Django
  • Postgres
  • Celery - for async worker jobs
  • Redis - cache and distributed key/value store

We make a number of technical trade-offs:

  • System designed for 10-100k samples, mostly exomes
  • Multi-sample analysis is done on samples from same VCF (ie we do not store bams or gVCFs)
  • Optimise for bioinformatician productivity vs raw performance

See also:

Variants

Variants from different VCFs are linked to a single database record. VCF sample data (zygosity/allele depth etc) are stored in partitioned tables, and packed into a single row (to reduce joins on multi-sample queries)

Patients

Annotation

Genes

Analysis

Users can make custom variant filters graphically by constructing a directed acyclic graph of Analysis Nodes which represent sources or filters of variants.

These filters work entirely in SQL (abstracted via Django Q objects) and so can be combined easily using logical operators and work in real time.

Classification

See https://shariant.readthedocs.io

Future work:

ClinVar-Export

Sequencing Data

Sequencing and QC is handled in the "seqauto" app.

Future work:

Issue #76: SeqAuto API - Code was written for a diagnostic intranet, runs jobs to crawl disks to load QC files and import VCFs. Move this code into scripts which call APIs.

Misc

Authentication

Database

Front End

Install

Configuration

Maintenance

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