Up: Component summary Component

VariantFilter

Filters 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,
controlThreshold=1,
chromosome=chr1,
metadata.timeout=0

test2 properties in annotationArray (missing) (missing) (missing)

caseThreshold=1,
controlThreshold=0,
chromosome=chr1,
metadata.timeout=0

test3_NA properties in annotationArray (missing) (missing) (missing)

caseThreshold=2,
controlThreshold=1,
chromosome=chr1,
metadata.timeout=0


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