We have just started genotyping with GSA in IScan and generated first idat files. To QC we were advices to use GenomeStudio and for that we downloaded all the necessary files: bpm, egt, imap files from illumina website. Yet when we performed analysis in Genomestudio, it returned 0.0000 call rate for all samples. The operator who came to teach us to use the instrument suggested that it might be because we performed analysis with Grch38 manifest files (bpm), so I ran the analysis again with GrCh37 manifest bpms yet the call rate remains 0. Any ideas on how to debug this issue?
Another question is that, prior to this I had GWAS analysis experience, but i had readily available bed, bim, fam files to start with. Could You please suggest how can we transfer our idat files to these formats? is that possible? or how else can we start GWAS analysis?