Up: Component summary
Up: Component summary
Component
VCF2CSVConverts variation calls in VCF format to CSV
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | VariationAnalysis |
| Authors | Sirkku Karinen (sirkku.karinen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml VCFConverter.java |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| vcf | VCF | Mandatory | VCF variation calls |
Outputs| Name | Type | Description |
|---|---|---|
| annotations | DNARegion | Variations are annotated to one file. |
| samples | Array<CSV> | Data from each sample. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| infoData | string | "DP=CombinedDepth" | Data that is extracted from the INFO column. Give also a column name for each extracted variables. |
| onlyAnnotations | boolean | false | If vcf file doesn't have the genotypes, onlyAnnotations=true will create only the annotations output. |
| sampleData | string | "DP=Depth" | Data that is extracted from the variation calls. Give also a column name for each extracted variables. |
| useIds | boolean | true | Use existing Ids in vcf files (true) or create new ids (false). |
Test cases| Test case | Parameters▼ | IN vcf |
OUT annotations |
OUT samples |
||
|---|---|---|---|---|---|---|
| case1 | properties | vcf | annotations | samples | ||
|
infoData=DP=CombinedDepth,AC=Example |
||||||
| case2 | properties | vcf | annotations | samples | ||
|
infoData=NS=Samples,END=End,CN=CopyNumber, |
||||||