Up: Component summary
Up: Component summary
Function
GenomicVariantAnnotatorQueries the Database of Genomic Variants. The connection is established via the URLInput component. The input table must contain an ID column, and columns for chromosome and locus for each ID.
The Database of Genomic Variants is a curated catalogue of structural variation in the human genome, variation which includes SNPs, tandem repeats and copy number variants.
| Version | 2.0 |
|---|---|
| Bundle | microarray |
| Categories | Annotation |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Source files | component.xml function.scala |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| inputT | CSV | Mandatory | Input file containing columns for chromosome and locus as specified in chrCol and locusCol parameters, respectively. |
Outputs| Name | Type | Description |
|---|---|---|
| table | CSV | Results of the query. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| chrCol | string | (no default) | Column for the chromosome identifier in the input. |
| endCol | string | (no default) | Column for the query locus end. |
| idCol | string | (no default) | IDcolumn in inputT file. |
| startCol | string | (no default) | Column for the query locus start. |
Test cases| Test case | Parameters▼ | IN inputT |
OUT table |
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|---|---|---|---|---|---|---|
| case1 | properties | inputT | table | |||
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chrCol=chr, |
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