Question: Illumina HumanOmniExpress IDAT files
0
gravatar for andrew.j.skelton73
4.3 years ago by
London
andrew.j.skelton735.8k wrote:

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, 

idat illumina • 2.9k views
ADD COMMENTlink modified 16 months ago by freeseek40 • written 4.3 years ago by andrew.j.skelton735.8k

After a bit of digging, I found the cram package, which seems to do what I want - Any other suggestions are welcome! 

ADD REPLYlink written 4.3 years ago by andrew.j.skelton735.8k
1
gravatar for freeseek
16 months ago by
freeseek40
freeseek40 wrote:

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 written 16 months ago by freeseek40
0
gravatar for niutster
3.4 years ago by
niutster80
niutster80 wrote:

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 written 3.4 years ago by niutster80

That paper is in reference to Methylation data, not Genotyping data.

ADD REPLYlink written 3.4 years ago by andrew.j.skelton735.8k
0
gravatar for jmzeng1314
2.7 years ago by
jmzeng131490
jmzeng131490 wrote:

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 written 2.7 years ago by jmzeng131490

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 written 2.7 years ago by andrew.j.skelton735.8k
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