Up: Component summary Component

VCF2CSV

Converts 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,
onlyAnnotations=true,
sampleData=


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