Based on https://github.com/Illumina/Nirvana/releases/tag/v2.0.10
This app runs Nirvana (v2.0.10) to annotate variants.
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).
This app should be executed stand-alone or as part of a DNAnexus workflow for a single sample.
The app requires a vcf file (.vcf) to run.
The app outputs a compressed JSON file (where [outPrefix] is the vcf filename without extension):
[outPrefix].json.gz - structured JSON representation of all annotation and sample information as extracted from the VCF
The app runs Nirvana using an input vcf file and uploads the output to DNAnexus.
Where insertion/deletion differences exist betweeen a RefSeq transcript and the reference genome sequences, Nirvana 2.0.3 generates incorrect HGVS nomenclature for variants downstream of those differences.