How to use the PLINK Report Plug in in GenomeStudio

GenomeStudio: How to use the PLINK Report Plug-in

Before beginning:

• Download the PLINK Input Report Plug-in v2.1.4 from Illumina's GenomeStudio v2.0 Plug-in website page and follow the instructions provided during installation to get started.

• Create or open an existing GenomeStudio project and follow the instructions below to use the PLINK plug-in.

1. Select Analysis > Reports > Report Wizard. The Report Wizard window opens.

1. Open the PLINK Input Report by selecting the Custom Report option.

Notes:

PedigreeFile (optional)

• A pedigree file is a tab-delimited file. It is not required if the “Mother ID” and the “Father ID” as well as the “Affected Status” columns are present in the Samples table.

• The report processes only sample IDs that appear in both the pedigree file and the genotyping project.

TraitDataFile (optional)

• The trait data file is a tab-delimited file. It includes the quantitative trait data with probe IDs in row 1 and sample IDs in column 1.

UseForwardStrand

• When generating the PLINK report from GenomeStudio, users have the option of choosing whether to report the alleles in "Forward" or Illumina "TOP" strand. In the Report Wizard dialog box that appears, there is an option called "UseForwardStrand", which users can either set to "True" or "False".

• If set true, then the report returns the alleles in "Forward" strand. If false, then the default report is created using Illumina's TOP strand alleles. Forward strands are assignments directly from the public database. All the sequences in a public data base, ie, NCBI dbSNP, come with a given forward (F) or reverse (R) designation. F and R strands are arbitrary designations by dbSNP and can change between release versions.

1. Optional: It is possible to adjust the algorithm input parameters from the GUI. Further, users can make permanent changes to the input parameters by editing the plug-in in the configuration file (PLINK Input Report Plug-in v2.1.4 for GenomeStudio Genotyping Module User Guide, 2016, p. 1).

2. Select Next and decide which SNPs to include in the report from the following options.

• Include zeroed SNPs in the report.

• Remove zeroed SNPs from the report.

  

1. Select Next to set the Output Path and the Report Name.

1. Select Finish to create the report. The GenomeStudio Progress Status window opens. After the report has finished processing, a new window appears and prompts the user to view the report.

2. Select Yes to display the location of the output file in a default Windows text viewer.

Note:

The file might be too large to open in the default Windows text viewer, eg, NotePad. As a workaround, the file can be opened in, for example, WordPad or NotePad++ instead.

The files created by the report include:

• .bat, a batch file that runs PLINK with a default set of input parameters listed in the script file.

• .map, the map file, showing base pair and position for each marker.

• .ped, the LINKAGE format input file.

• .phenotype, a text file which lists the quantitative trait data for eachsample.

• .script, a text file which lists the input parameters to be used by thePLINK executable.

Note:

The sample gender is determined using the Gender column in the Samples table.

For more information, the User Guide is available in the PLLINK Input Report Plug-in v2.1.4 installer folder on GenomeStudio 2.0 Plug-in website page.