Making Finalreports

Generating FinalReports in GenomeStudio

Open the project

All the samples should be in the same project, however this is not essential. It is highly recommended that you recluster your data as this reduces noise and improves genotyping and CNV prediction accuracy, however it will not affect the identity program.

Double click on the project file.

FinalReport Step 1

On the menu bar, select 'Analysis'.

In the submenu choose 'Reports'.

Select 'Report Wizard'.

Bead1.jpg

FinalReport Step 2

From the list select the 'Final Report', then press 'Next >'.

Bead2.jpg

FinalReport Step 3

The FinalReport must be in the correct format with the columns in the right order. You will need to check/change three settings:

#Check the 'Standard' radio button at the top is selected (not 'Matrix' or '3rd party').
#Select to show ONLY ten 'Displayed Fields'; they must be in this order:
##SampleID
##SNP Name
##Chr
##Position
##Allele1 – Top
##Allele2 – Top
##Theta
##R
##B Allele Freq
##Log R Ratio
#Check the 'Sample' radio button is selected rather than 'SNP'
#Check the 'Tab' radio button is selected rather than 'comma'
#Change the number of 'Samples / File' to '1'

Press 'Next >'.

Bead3.jpg

FinalReport Step 4

Select a directory for your output files and any name for the 'Report Name'. You must keep the suffix 'FinalReport' otherwise the files will not be recognised by the identity program.

Click 'Finish' and wait while the FinalReports are generated. These files are big (about 40Mb per sample for a 1M chip) and take several hours to be created for large projects with hundreds of samples.

Bead4.jpg

Check header

The top of the finished resulting FinalReport should look like this:

FR_format.jpg
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