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  • SnpEff Annotation and Filtration Element

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Type: seff

ParameterParameter in the GUIType
out-modeOutput directory

booleanstring

inp-formatInput formatbooleanstring
out-format
Output formatbooleanstring
genome
Genomenumericstring
updown-lengthUpstream/downstream lengthnumeric
canonCannonical transcriptsboolean
hgvs
HGVS nomenclaturestringboolean
lofAnnotate loss of functionstringboolean
motifAnnotate TFBSs motifsnumeric

 

const QString SnpEffWorker::BASE_SNPEFF_SUBDIR = "snpeff";
const QString SnpEffWorker::INPUT_PORT = "in-file";
const QString SnpEffWorker::OUTPUT_PORT = "out-file";
const QString SnpEffWorker::OUT_MODE_ID = "out-mode";
const QString SnpEffWorker::CUSTOM_DIR_ID = "custom-dir";

const QString SnpEffWorker::INPUT_FORMAT = "";
const QString SnpEffWorker::OUTPUT_FORMAT = "";
const QString SnpEffWorker::GENOME = "";
const QString SnpEffWorker::UPDOWN_LENGTH = "";

const QString SnpEffWorker::CANON = "";
const QString SnpEffWorker::HGVS = "";
const QString SnpEffWorker::LOF = "";
const QString SnpEffWorker::MOTIF = "";

const QString SnpEffFactory::ACTOR_ID("seff");

boolean

Input/Output Ports

The element has input portsport:

Name in GUI: Input assembly Variations

Name in Workflow File: in-assembly

Slots:

Slot In GUISlot in Workflow FileType
Dataset namedatasetstring
Source urlurlstring

Name in GUI: Input sequences

Name in Workflow File: in-sequencefile

Slots:

Slot In GUISlot in Workflow FileType
Source urlurlstring

And 1 output port:

Name in GUI: Output  Annotated variations

Name in Workflow File: out-variationsfile

Slots:

Slot In GUISlot in Workflow FileType
Variation trackvariation-trackSource urlurlvariation