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SnpEff eff: (version 4.5covid19)

Sequence changes (SNPs, MNPs, InDels):

Input format:

Select an annotated Coronavirus genome:

Output format:

Create CSV report, useful for downstream analysis (-csvStats):

Upstream / Downstream length:

Annotation options:

Use custom interval file for annotation:

Only use the transcripts in this file:

Format is one transcript ID per line

Filter output:

Filter out specific Effects:

Chromosomal position:

Text to prepend to chromosome name:

By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. You can prepend any string you want to the chromosome name

Produce Summary Stats:

Suppress reporting usage statistics to server:

What it does

This is a special edition of SnpEff tweaked for SARS-CoV-2 variant annotation.

SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).

A typical SnpEff use case would be:

Input: The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF).

Output: SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes).

Databases in the SnpEff Covid-19 edition

This special version of SnpEff provides only a fixed number of SARS-CoV-2-related genome databases.

Unlike with regular SnpEff releases, it is not possible to extend this set, i.e, you cannot download additional databases or build custom databases for this edition.

To learn more about SnpEff read its manual at http://snpeff.sourceforge.net/SnpEff_manual.html