Question: IDAT to VCF conversion
0
gravatar for karthick.n
9 months ago by
karthick.n10
karthick.n10 wrote:

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

ADD COMMENTlink modified 5 months ago by curious470 • written 9 months ago by karthick.n10

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

ADD REPLYlink written 9 months ago by GenoMax95k

Thanks for your response!

ADD REPLYlink written 9 months ago by karthick.n10
0
gravatar for Lemire
9 months ago by
Lemire600
Canada
Lemire600 wrote:

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

ADD COMMENTlink written 9 months ago by Lemire600

Thanks a lot for your response!

Regards, Karthick

ADD REPLYlink written 9 months ago by karthick.n10
0
gravatar for curious
5 months ago by
curious470
curious470 wrote:
  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

ADD COMMENTlink modified 5 months ago • written 5 months ago by curious470
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 964 users visited in the last hour
_