Up: Component summary Component

LocationVariation

Gets variation from Ensembl from a genomic location.

Version 1.0
Bundle microarray
Categories Annotation
Authors Sirkku Karinen (sirkku.karinen@helsinki.fi)
Issue tracker View/Report issues
Requires asser.jar (jar) ; mysql-connector-java-5.1.6-bin.jar (jar)
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
locations CSV Mandatory Locations having chromosome, start and end.
variationDatabase Properties Mandatory Database properties

Outputs

Name Type Description
variations CSV Variations mapped for given locations.
populations CSV Allele frequencies and presence in different populations. This output is optional and will be created if parameter getFreq is true.

Parameters

Name Type Default Description
chromosome string "chromosome" Reference column name
end string "" End column name. Optional.
getFreq boolean false Get populations output
location2variation boolean true Mapping from location to variation (=true) or from variation to location (=false)
population string "*" Population name, or a part of name, like 'CEU' or comma separated list of names like 'CEU,1000genomes'. * is all.
rowRange string "*" Example 100-250, range of rows that need to be processed. * is all rows. Rows start from 1.
rsId string "" RsId column name.
start string "start" Start column name. Only start position is allowed when variation has length of 1 (in the case of SNPs).

Test cases

Test case Parameters IN
locations
IN
variationDatabase
OUT
variations
OUT
populations
case1 properties locations variationDatabase variations populations

chromosome=chr,
start=pos,
getFreq=true,
population=CEU,JPT

case2 properties locations variationDatabase variations populations

chromosome=chr,
start=pos,
rowRange=2-2

case3_rsId properties locations variationDatabase variations populations

location2variation=false,
rsId=StartMarker


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