Galaxy | (sandbox for testing) |

SnpEff (version 3.3)

Sequence changes (SNPs, MNPs, InDels):

Input format:

Output format:

Genome:

Upstream / Downstream length:

Set size for splice sites (donor and acceptor) in bases. Default: 2:

Filter homozygous / heterozygous changes:

Filter sequence changes:

Annotation options:

Non-coding and regulatory Annotation:

These are available for only a few genomes

Use custom interval file for annotation:

Only use the transcripts in this file. Format: One transcript ID per line.:

Filter output:

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:

Do not report usage statistics to server:

This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.

For details about this tool, please see the snpEff web site.