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Nirvana Documentation

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https://illumina.github.io/NirvanaDocumentation/

Documentation for Nirvana, a C# and .NET Core-based variant annotation tool. It includes technical specifications for the Nirvana JSON file format, guidance on incorporating custom annotations, and details on integrated data sources such as gnomAD, ClinVar, COSMIC, and SpliceAI. The docs cover version 3.2.5 through 3.19 (unreleased) and include utilities like the Jasix index for TABIX-like indexing of JSON output.

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What's inside Nirvana

  2. Overview of Nirvana genomic variant annotation

    Nirvana is a clinical-grade annotator for genomic variants, including SNVs, MNVs, insertions, deletions, indels, STRs, gene fusions, and Structural Variants (SVs) such as CNVs. It accepts VCF files as input and produces a structured JSON representation containing all annotations and sample information. It is designed to handle multiple alternate alleles and multiple samples. Nirvana can be deployed as a stand-alone package, as an AWS Lambda function, or integrated into larger software tools.

  3. Overview of Nirvana genomic variant annotation

    Nirvana is a clinical-grade annotator for genomic variants, including SNVs, MNVs, insertions, deletions, indels, STRs, gene fusions, and SVs (including CNVs). It can be deployed as a stand-alone package, an AWS Lambda function, or integrated into larger software tools. Nirvana supports multiple alternate alleles and multiple samples.

  4. Overview of SAUtils for Nirvana Annotation

    SAUtils is a utility tool designed to convert original genomic data files (such as VCFs, TSVs, XML, and HTML) from various sources (e.g., ClinVar, dbSNP, gnomAD) into binary supplementary annotation files. These binary files are then used by the Nirvana Annotation engine to provide supplementary annotations in the output.

  5. Overview of SAUtils for Nirvana Annotation

    SAUtils is a utility tool designed to create binary supplementary annotation files (such as .nsa, .gsa, .npd, and .nsi) from original data files (e.g., VCFs, TSVs, XML, HTML). These binary files are used by the Nirvana Annotation engine to provide supplementary annotations in the final output. It supports a wide range of data sources including ClinVar, dbSNP, gnomAD, COSMIC, and others.

  6. Overview of Nirvana genomic variant annotation

    Nirvana is a clinical-grade genomic variant annotator designed to handle SNVs, MNVs, insertions, deletions, indels, STRs, gene fusions, and Structural Variants (SVs), including Copy Number Variants (CNVs). It accepts VCF files as input and produces a structured JSON representation of all annotations and sample information. Nirvana supports multiple alternate alleles and multiple samples. It can be deployed as a stand-alone package, an AWS Lambda function, or integrated into larger software tools.

  7. Overview of Primate AI pathogenicity scores

    Primate AI is a deep residual neural network used to classify the pathogenicity of missense mutations. The tool provides raw scores that are biased by gene context; therefore, it is recommended to aggregate these scores as percentiles relative to the associated gene. Research suggests the 25th percentile serves as a proxy for benign variants and the 75th percentile as a proxy for pathogenic variants.

  8. Overview of Primate AI for missense mutation pathogenicity

    Primate AI is a deep residual neural network used to classify the pathogenicity of missense mutations. The method is based on the research published in 'Predicting the clinical impact of human mutation with deep neural networks' (Nat Genet 50, 1161–1170, 2018).

  9. Overview of Primate AI Pathogenicity Scoring

    Primate AI is a deep residual neural network used to classify the pathogenicity of missense mutations. It provides raw scores that are biased by gene context; therefore, it is recommended to aggregate these scores as percentiles relative to the associated gene. Research suggests the 25th percentile serves as a proxy for benign variants and the 75th percentile as a proxy for pathogenic variants.

  10. Overview of Nirvana genomic variant annotation

    Nirvana is a clinical-grade annotator for genomic variants, including SNVs, MNVs, insertions, deletions, indels, STRs, gene fusions, and SVs (including CNVs). It can be deployed as a stand-alone package, an AWS Lambda function, or integrated into larger software tools. Nirvana accepts VCF files as input and produces a structured JSON representation of all annotation and sample information, supporting multiple alternate alleles and multiple samples.

  11. Overview of Nirvana genomic variant annotation

    Nirvana is a clinical-grade genomic variant annotator designed for accuracy and regulatory compliance. It supports a wide range of variant types, including SNVs, MNVs, insertions, deletions, indels, STRs, gene fusions, and structural variants (SVs), including CNVs.

    Nirvana can be deployed as a stand-alone package, as an AWS Lambda function, or integrated into larger software tools. It accepts VCF files as input and produces a structured JSON representation containing all annotations and sample information, supporting multiple alternate alleles and multiple samples.

  12. Overview of Nirvana genomic variant annotation

    Nirvana is a clinical-grade annotator for genomic variants, including SNVs, MNVs, insertions, deletions, indels, STRs, gene fusions, and Structural Variants (SVs) such as Copy Number Variations (CNVs). It can be deployed as a stand-alone package, an AWS Lambda function, or integrated into larger software tools. Nirvana supports multiple alternate alleles and multiple samples per input.