Are there any GenomeStudio alternatives to process Illumina genotyping array?
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2.3 years ago
Zhenyu Zhang ▴ 450

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

genomestudio genotyping array illumina • 1.7k views
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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?

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

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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.

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2.2 years ago

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.

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23 months ago
freeseek ▴ 120

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

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