Up: Component summary
Up: Component summary
Component
VariantFilterFilters variants based on allele frequencies in the data
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | VariationAnalysis |
| Authors | Sirkku Karinen (sirkku.karinen@helsinki.fi) |
| Issue tracker | View/Report issues |
| Source files | component.xml VariantFilter.java |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | Array<CSV> | Mandatory | Array of sample variation files |
| annotationArray | Array<CSV> | Optional | Variation annotation files separately for each sample. Annotations need to be indexed according to sample indices. Either annotations or annotation input needs to be given. |
| annotation | CSV | Optional | Variation annotation file that annotates all the variants in all the samples. Either annotations or annotation input needs to be given |
Outputs| Name | Type | Description |
|---|---|---|
| out | Array<CSV> | Filtered samples. |
| alleleCount | CSV | Number of alleles. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| acForAll | boolean | true | Output allele count for all variants (true) or only for variants that were included to output (false). |
| caseThreshold | int | (no default) | Minimum number of times the allele of the variant needs to be seen in cases. |
| cases | string | "case" | Regular expression to identify cases from sample names. |
| chromosome | string | (no default) | Which chromosome to process. |
| controlThreshold | int | (no default) | Maximum number of times the allele of the variant can be seen in controls. |
| controls | string | "control" | Regular expression to identify controls from sample names. |
| sampleNames | string | "" | Comma-separated list of sample names to name output, if empty, uses input port sample indecies. |
| sampleThreshold | int | -1 | Minimum number of case samples that have allele. |
Test cases| Test case | Parameters▼ | IN in |
IN annotationArray |
IN annotation |
OUT out |
OUT alleleCount |
|---|---|---|---|---|---|---|
| test1 | properties | in | annotationArray | (missing) | out | (missing) |
|
caseThreshold=2, |
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| test2 | properties | in | annotationArray | (missing) | (missing) | (missing) |
|
caseThreshold=1, |
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| test3_NA | properties | in | annotationArray | (missing) | (missing) | (missing) |
|
caseThreshold=2, |
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