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IDAT to VCF conversion

Hi,

I am working on array data and it's a illumina Infinium based array. But in my case it's a customized kit so i don't have a cluster file for the idat to gtc file conversion. But I have idat file and bpm file. Can anyone help me on this ? Is there any way to process the idat file without cluster file?

Regards, Karthick

arraysequencing idat cluster genomestudio
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updated by curious curious • written by karthick.n • karthick.n

Not sure if freeseek will work without cluster file. But worth a try.

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written by GenoMax GenoMax

2 answers

Thanks a lot for your response!

Regards, Karthick

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written by karthick.n • karthick.n

  1. You can do the clustering to get a cluster file, assuming there is enough samples to do a good job, and export as reports then convert to VCF using scripting. This is a ton of work.

  2. You can recluster in GS then use the plink export plugin then use plink to convert to VCF too. This is probably the fastest way to get a VCF from GS that I know of

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written by curious curious

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