Hello everybody
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?
Thank You
Coordinates in the manifest .bpm file are not used in the conversion from IDAT to GTC. Most likely you have a faulty .egt cluster file, if I had to guess. Can you install gtc2vcf from here (binaries here) and run the following command on one of the GTC files with 0.0000 call rate?
Thanks for You reply. The issue is that, our analysis didnot generate any gtc files. Could You please share the path on how to do it? Is there any way to do it without genome studio?
The documentation here will teach you how to do all the steps without using GenomeStudio (except generating an .egt cluster file) using Illumina's iaap-cli and BCFtools/gtc2vcf
You have Illumina genotyping array files in idat format - this is understood. Please provide at least 2 of these files to us so that we can properly address your question.
Can i share the files here?