Are there any GenomeStudio alternatives to process Illumina genotyping array?

Question

[Zhenyu Zhang]

The mouse clicking interface of GenomeStudio is so unfriendly for large and continuous data production. - Do we have alternatives to this that can process Illumina genotyping array idat files? - Or do you have any suggestions to automate the GenomeStudio process with command lines? Thanks

[curious]

I am basically in the same spot. I just started looking at genomestudio today, so I have not dug very deep yet. I'm sure they worked really hard on this, but a windows only GUI bioinformatics tool is a bit odd. Did you end up coming across any alternatives?

[Zhenyu Zhang]

It seems some basics can be done with GS command lines, but still in windows.

[curious]

Did you do this? I poked around genomestudio. I see an option to use c# scripts but can find no information at all about using this functionality through googling. I want to do some manipulations to the full data table before exporting, but for the life of me can't find a way to do that within gneomestudio.

[Joel Wallenius]

Hey, did you find a good solution? I've just been tasked with GenomeStudio...

Answer 1

[steffanchristiansen]

The crlmm package in R should be able to do it. However, in my own experience it is difficult to run it for Omni5 generated data. I guess it depends on which genotype array you are using. Alternatively, beadarray should also be able to read idat files but I have not tried that package yet.

Answer 2

[Giulio Genovese]

You can use Illumina proprietary GenCall algorithm to generate GTC files out of IDAT file, there are now two approaches:

(i) using the Illumina Array Analysis Platform

(ii) using the Illumina Beeline/AutoConvert software

I describe how to use either approach on Linux here

[Joel Wallenius]

Hey, is this still the "official" approach if not wanting to use GenomeStudio?

Answer 3

[Zhenyu Zhang]

as mentioned above, some basic functions can be done in command line in windows.