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SnpEff¹ is a variant annotation and effect prediction tool that requires its own variant annotation files, separate to the other Variant annotation library files. If you wish to use SnpEff, library files need to be added to this section.

VEP database

The Ensembl Variant Effect Predictor (VEP) is another variant annotation and prediction tool that requires its own annotation files, separate to the Variant annotation library files. If you wish to use VEP, library files need to be added to this section.

Annotation models

This section includes two types of library file: annotation models & aligner indexes.

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Annotation models are used for quantification in gene expression analyses, annotating detected variants (e.g. to predict amino acid changes), visualizations in Chromosome view, generating coverage reports and for aligner index creation (see Adding Aligner Indexes Based on an Annotation Model). Typical file formats include GTF, GFF, GFF3 and BED.

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