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Parameters

ParameterParameter in the GUITypeout-modeOutput directory

string

inp-formatInput formatstringout-format
Output formatstringgenome
Genomestringupdown-lengthUpstream/downstream lengthnumericcanonCannonical transcriptsbooleanhgvs
HGVS nomenclaturebooleanlofAnnotate loss of functionboolean

Parameter	Description	Default value	Parameter in Workflow File	Type
Output directory	Select 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	out-mode	string
Input format	Select the input format of variations.	VCF	inp-format	string
Output format	Select the format of annotated output files.	VCF	out-format	string
Genome	Select 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	genome	string
Upstream/downstream length	Upstream and downstream interval size. Eliminate any upstream and downstream effect by using 0 length.	No upstream/downstream interval (0 bases)	updown-length	numeric
Cannonical transcripts	Use only cannonical transcripts.	False	canon	boolean
HGVS nomenclature	Annotate using HGVS nomenclature.	False	hgvs	boolean
Annotate loss of function	Annotate Loss of function (LOF) and Nonsense mediated decay (NMD).	False	lof	boolean
Annotate TFBSs motifs	Annotate transcription factor binding site motifs (only available for latest GRCh37).	False

Parameters in Workflow File

Type: seff

The element has 1 input port:

Name in GUI: Variations

Name in Workflow File: in-file

Slots:

And 1 output port:

Name in GUI: Annotated variations

Name in Workflow File: out-file

Slots: