Illumina HumanOmniExpress IDAT files

Question

[andrew.j.skelton73]

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

[andrew.j.skelton73]

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

[Tang.shifang]

Hello, did you know how to read IDAT files in R? and how about the script? I tried to use read.idat, but there always were error:

Error in `[.data.frame`(bgx$controls, , c("Probe_Id", "Array_Address_Id")) : 
  undefined columns selected

or

Error in open.connection(file, "rt") : cannot open the connection
In addition: Warning message:
In open.connection(file, "rt") :
  cannot open compressed file 'HumanHT-12_V4_0_R2_15002873_B_WGDASL.bgx', probable reason 'No such file or directory'

Looking forward to your reply. and many thanks!

P.S.: I cannot use Genome Studio software, that's why only R I can use.

Answer 1

[Giulio Genovese]

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.

Answer 2

[niutster]

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.

[andrew.j.skelton73]

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

Answer 3

[jmzeng1314]

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.

[andrew.j.skelton73]

Genome Studio is proprietary software, and not open source. I mention in the OP that I was looking for alternatives to Genome Studio.