PLINK export plugin GenomeStudio

Question

[Sreya]

Hi,

We analysed ~1300 samples from Illumina HumanCoreExome 24 v.1.0 chip, calling the variants using GenomeStudio. We wish to do further analysis using the PLINK software suite, for which I exported the data using the PLINK data export plugin available for GenomeStudio. I selected the option in the plugin, which enables conversion of data to forward strand. However, on examination it was found that several 1000s of SNPs were not in the forward strand. What could be the reason for this? Is there a way to get the data in forward strand? There isn't much information on the plugin online.

-Sreya

Answer 1

[SpacemanSpiffo]

I'm 3 and a half years late to this but for anyone else who stumbles upon this page - this is almost certainly due to the really confusing naming system in Illumina's GenomeStudio - the "forward allele" column in the software doesn't mean what it normally means. To get the column normally thought of as the "forward strand" allele, you need to use the "plus" column.

Edit: correct me if I'm wrong but looks like the "plus" column is not supported in the plink plugin for GenomeStudio