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Annotates and filters variations with SnpEff.

Element type: seff


ParameterDescriptionDefault valueParameter in Workflow FileType
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 fileout-mode


Input formatSelect the input format of variations. VCFinp-formatstring
Output formatSelect the format of annotated output files. VCFout-format
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 sapiensgenome
Upstream/downstream lengthUpstream and downstream interval size. Eliminate any upstream and downstream effect by using 0 length.No upstream/downstream interval (0 bases)updown-lengthnumeric
Cannonical transcriptsUse only cannonical transcripts.Falsecanonboolean
HGVS nomenclatureAnnotate using HGVS nomenclature.Falsehgvs
Annotate loss of functionAnnotate Loss of function (LOF) and Nonsense mediated decay (NMD).Falselofboolean
Annotate TFBSs motifsAnnotate transcription factor binding site motifs (only available for latest GRCh37).Falsemotifboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Variations

Name in Workflow File: in-file


Slot In GUISlot in Workflow FileType
Source urlurlstring

And 1 output port:

Name in GUI: Annotated variations

Name in Workflow File: out-file


Slot In GUISlot in Workflow FileType
Source urlurlvariation
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