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Question: Illumina HumanOmniExpress IDAT files
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Hi,

I've got some Illumina HumanOmniExpress Genotyping Chip IDAT files and I was wondering if there are any packages that people know of that can read them? Are the IDAT files for this chip encrypted to a point where I'd have to use genome studio?

Thanks,

ADD COMMENTlink 4.6 years ago andrew.j.skelton73 5.7k • updated 19 months ago freeseek • 40
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After a bit of digging, I found the cram package, which seems to do what I want - Any other suggestions are welcome!

ADD REPLYlink 4.6 years ago
andrew.j.skelton73
5.7k
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I wrote gtc2vcf, a high performing bcftools plugin to convert Illumina GTC files to VCF on Linux. It can also be made to work with IDAT files. Some features are currently missing (as of 2018-07-11) but I plan to include them in the future if there is demand.

ADD COMMENTlink 19 months ago freeseek • 40
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Hi,

There are several packages you can use them. Refer to "Review of processing and analysis methods for DNA methylation array data" paper. In this paper you can find them.

ADD COMMENTlink 3.7 years ago niutster • 80
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That paper is in reference to Methylation data, not Genotyping data.

ADD REPLYlink 3.7 years ago
andrew.j.skelton73
5.7k
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The same question : how to analysis HumanOmni5 Exome-4v1-2 Array data ?

you can just use Genome Studio to analysis IDAT files, but you should figure out their original file names.

ADD COMMENTlink 3.0 years ago jmzeng1314 • 90
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Genome Studio is proprietary software, and not open source. I mention in the OP that I was looking for alternatives to Genome Studio.

ADD REPLYlink 3.0 years ago
andrew.j.skelton73
5.7k

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