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.