Workflow Designer Documentation v. 33
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  • SnpEff Annotation and Filtration Element
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Annotates and filters variations with SnpEff.

Parameters in GUI

ParameterDescriptionDefault value
Output directorySelect an output directory. Custom - specify the output directory in the 'Custom directory' parameter. Workflow - internal workflow directory. Input file - the directory of the input file.Input file
Input formatSelect the input format of variations. VCF
Output formatSelect the format of annotated output files. VCF
GenomeSelect the target genome from the list of SnpEff databases. Genome data will be downloaded if it is not found. The list of databases depends on the SnpEff external tool version.Homo sapiens
Upstream/downstream lengthUpstream and downstream interval size. Eliminate any upstream and downstream effect by using 0 length.No upstream/downstream interval (0 bases)
Cannonical transcriptsUse only cannonical transcripts.False
HGVS nomenclatureAnnotate using HGVS nomenclature.False
Annotate loss of functionAnnotate Loss of function (LOF) and Nonsense mediated decay (NMD).False
Annotate TFBSs motifsAnnotate transcription factor binding site motifs (only available for latest GRCh37).False

Parameters in Workflow File

Type: seff

ParameterParameter in the GUIType
out-modeOutput directory

string

inp-formatInput formatstring
out-format
Output formatstring
genome
Genomestring
updown-lengthUpstream/downstream lengthnumeric
canonCannonical transcriptsboolean
hgvs
HGVS nomenclatureboolean
lofAnnotate loss of functionboolean
motifAnnotate TFBSs motifsboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Variations

Name in Workflow File: in-file

Slots:

Slot In GUISlot in Workflow FileType
Source urlurlstring

And 1 output port:

Name in GUI: Annotated variations

Name in Workflow File: out-file

Slots:

Slot In GUISlot in Workflow FileType
Source urlurlvariation
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