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Plink

Wraps Plink software that allows various genome wide SNP data manipulations and analyzes. Some functions are predefined and can be run using functionType parameter. Also other commands can be executed. Many of the Plink text-format outputs are easily transformed into csv-format to be further used in the Anduril-workflow. Text2CSV-component in the Anduril beta-bundle can be used for the transformation.

Version 1.1
Bundle microarray
Categories SNP
Authors Sirkku Karinen (sirkku.karinen@helsinki.fi)
Issue tracker View/Report issues
Requires plink ; installer (bash)
Source files component.xml
Usage Example with default values

Inputs

Name Type Mandatory Description
pedFile TextFile Mandatory SNP-data in ped format. http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped
mapFile TextFile Optional Map file for annotating SNPs in ped-file. If no map file is given, Plink uses map file that is in the same directory with ped file AND is named in the same fashion i.e. myPedFIle.ped and myPedFile.map. If binary files are in use, map file needs to be given in this way.
file1 BinaryFile Optional Additional file that can be given to command is referred as @f1@ in the command
file2 BinaryFile Optional Additional file that can be given to command is referred as @f2@ in the command
file3 BinaryFile Optional Additional file that can be given to command is referred as @f3@ in the command

Outputs

Name Type Description
result1 TextFile One of following predefined result files are put into this output port (if command is used): ld : plink.ld haploblock : plink.blocks hardy : plink.hwe
result2 TextFile One of following predefined result files are put into this output port (if command is used): haploblock : plink.blocks.det
result3 TextFile
result4 TextFile
result5 TextFile

Parameters

Name Type Default Description
Plink string "/opt/share/plink/plink" Path to Plink-program. This default is for CSBL old server. Gives Java IOException if this path not set correctly.
dataType string "text" Type of the input ped file text/binary
functionType string (no default) Plink command: ld : linkage (r2) calculation http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml#ld2 haploblock : haplotype block estimation http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml#blox hardy : calculation of Hardy-Weinberg statistics http://pngu.mgh.harvard.edu/~purcell/plink/thresh.shtml#hwd custom : parameters-parameter defines the Plink-command
outputFiles string "" Comma separated list of filenames that (custom) Plink commad produces. (plink.ped, plink.map, plink.freq,....see manual) These files will be inserted into output ports (result1,2...5) in the same order as they are in this list. This parameter is not used in predefined analyzes (ld,haploblock,hardy...)
parameters string "" Either additional parameters or full Plink command. EXAMPLES 1) Select samples and create new dataset. (use with parameter outputFiles="plink.ped,plink.map"): --keep /file/path/list_of_samples.csv --recode. 2) Calculate allele frequencies (use with parameter outputFiles="plink.frq") :--freq

Test cases

Test case Parameters IN
pedFile
IN
mapFile
IN
file1
IN
file2
IN
file3
OUT
result1
OUT
result2
OUT
result3
OUT
result4
OUT
result5
case1 properties pedFile mapFile (missing) (missing) (missing) (missing) result2 result3 result4 result5

functionType = ld

case2 properties pedFile mapFile (missing) (missing) (missing) result1 result2 result3 result4 result5

functionType = hardy

case3 properties pedFile mapFile (missing) (missing) (missing) result1 result2 result3 result4 result5

functionType = custom,
parameters = --linear,
outputFiles = plink.assoc.logistic


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