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Illumina Annotation Engine

Illumina Annotation Engine (IAE), also known as Nirvana, annotates variants, populating the following INFO fields in the gVCF file. For more information, visit https://github.com/Illumina/Nirvana/wiki.

Column

Description

CSQT

Contains the following values:

• Genotype index
• HGNC gene symbol
• Transcript ID
• Sequence ontology consequences

CSQR

Contains the following values:

• Genotype index
• Regulatory region ID
• Sequence ontology consequences

AF1000G

The allele frequency from all populations of 1000 genomes data.

AA

The inferred allele ancestral when it is from the chimpanzee or human lineage.

GMAF

The global minor allele frequency.

cosmic

The numeric identifier for the variant in the Catalogue of Somatic Mutations in Cancer (COSMIC) database.

clinvar

Clinical significance.

EVS

The allele frequency, coverage, and sample count from the Exome Variant Server (EVS).

RefMinor

The position where a reference base is a minor allele and annotated as a variant.

phyloP

The phyloP conservation score.

For Research Use Only. Not for use in diagnostic procedures. 

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