Question: Are there any GenomeStudio alternatives to process Illumina genotyping array?
gravatar for Zhenyu Zhang
16 months ago by
Zhenyu Zhang270
United States
Zhenyu Zhang270 wrote:

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

ADD COMMENTlink modified 11 months ago by freeseek100 • written 16 months ago by Zhenyu Zhang270

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?

ADD REPLYlink written 15 months ago by curious460

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

ADD REPLYlink written 15 months ago by Zhenyu Zhang270

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.

ADD REPLYlink written 12 months ago by curious460
gravatar for steffanchristiansen
14 months ago by
University of Copenhagen
steffanchristiansen0 wrote:

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.

ADD COMMENTlink written 14 months ago by steffanchristiansen0
gravatar for freeseek
11 months ago by
freeseek100 wrote:

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

ADD COMMENTlink written 11 months ago by freeseek100
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