Michael Strömberg edited this page Oct 12, 2017 · 32 revisions

Nirvana provides clinical-grade annotation of genomic variants (SNVs, MNVs, insertions, deletions, indels, and SVs (including CNVs). It can be run as a stand-alone package or integrated into larger software tools that require variant annotation.

The input to Nirvana are VCFs and the output is a structured JSON representation of all annotation and sample information (as extracted from the VCF). Optionally, a subset of the annotated data is available in VCF and/or gVCF files. Nirvana handles multiple alternate alleles and multiple samples with ease.

The software is being developed under a rigorous SDLC and testing process to ensure accuracy of the results and enable embedding in other software with regulatory needs. Nirvana uses a continuous integration pipeline where millions of variant annotations are monitored against baseline values on a daily basis.

Backronym: NImble and Robust VAriant aNnotAtor

Table of Contents

Link Description
Getting Started Everything you need to know about using Nirvana
Release Notes Release notes for each build
Design Documents Documentation on output file formats, etc.
Developer Guide Development protocols and special build instructions

What does Nirvana annotate?

For each alternate allele: For each sample:
  • positional information
    • chromosome & position
    • cDNA
    • CDS
    • protein
  • allelic information
    • reference & alternate alleles
    • ancestral allele
    • global minor allele & frequency
    • flag if this is a reference minor allele
  • identifiers
    • transcript
    • protein
    • gene
    • HGNC gene symbols
  • consequence (sequence ontology)
  • variant type (e.g. SNV, MNV, indel, etc.)
  • regulatory regions
  • protein function prediction (SIFT & PolyPhen)
  • affected introns & exons
  • HGVS coding and protein nomenclature
  • genotype
  • genotype quality
  • allele depths
  • total depth
  • variant frequency
  • Using the CANVAS CNV caller:
    • copy number
    • loss of heterozygosity

In addition we include data from the following external data sources:

  • dbSNP
  • 1000 Genomes Project
  • EVS
  • ExAC
  • phyloP conservation score
  • ClinVar
  • COSMIC
  • DGV

Licensing

Code

Nirvana source code is provided under the GPLv3 license. Nirvana includes several third party packages provided under other open source licenses, please see Dependencies for additional details.

Data

The data used by Nirvana is largely publicly available, however some data sources have special restrictions on use by non-academic entities.

Team Members

Michael Strömberg Rajat Shuvro Roy Yu Jiang
Project Lead Lead Developer Developer
Shuli Kang Julien Lajugie Haochen Li
Developer Lead Tester Tester
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.