IDAT to VCF conversion

Question

[karthick.n]

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

[GenoMax]

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

[karthick.n]

Thanks for your response!

Answer 1

[Lemire]

Chapter 6 of GenomeStudio Genotyping module guide deals with cluster generation.

https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/genomestudio/genomestudio-2-0/genomestudio-genotyping-module-v2-user-guide-11319113-01.pdf

[karthick.n]

Thanks a lot for your response!

Regards, Karthick

Answer 2

[curious]

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