Annotates and filters variations with SnpEff.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| 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 |
| Input format | Select the input format of variations. | VCF |
| Output format | Select the format of annotated output files. | VCF |
| Genome | Select the target genome. Genome data will be downloaded if it is not found. | Homo sapiens |
| Upstream/downstream length | Upstream and downstream interval size. Eliminate any upstream and downstream effect by using 0 length. | No upstream/downstream interval (0 bases) |
| Cannonical transcripts | Use only cannonical transcripts. | False |
| HGVS nomenclature | Annotate using HGVS nomenclature. | False |
| Annotate loss of function | Annotate Loss of function (LOF) and Nonsense mediated decay (NMD). | False |
| Annotate TFBSs motifs | Annotate transcription factor binding site motifs (only available for latest GRCh37). | False |
Parameters in Workflow File
Type: seff
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| out-mode | Output directory | booleanstring |
| inp-format | Input format | booleanstring |
| out-format | Output format | booleanstring |
| genome | Genome | numericstring |
| updown-length | Upstream/downstream length | numeric |
| canon | Cannonical transcripts | boolean |
| hgvs | HGVS nomenclature | stringboolean |
| lof | Annotate loss of function | stringboolean |
| motif | Annotate TFBSs motifs | numeric |
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 2 1 input portsport:
Name in GUI: Input assembly Variations
Name in Workflow File: in-assembly
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Dataset name | dataset | string |
| Source url | url | string |
Name in GUI: Input sequences
Name in Workflow File: in-sequencefile
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Source url | url | string |
And 1 output port:
Name in GUI: Output Annotated variations
Name in Workflow File: out-variationsfile
Slots:
| Slot In GUI | Slot in Workflow File | Type | |
|---|---|---|---|
| Variation track | variation-trackSource url | url | variation |