Is there a tool to transform GenomeStudio genotype format to VCF?

Question

[Leonor Palmeira]

I have genotyping data coming from GenomeStudio (Illumina) software from a SNP-chip, and I would like to convert this data to VCF. Does anyone know of a tool to do this? or should I write my own script to do this?

Here is how the GenomeStudio output file is formatted:

Index    Name           Address      Chr    Position     GenTrain Score   Sample1 Sample2
1        cnvi0000001    124680304    5      164388439    0                AA      AB
...

Answer 1

[Matt Shirley]

Genomestudio has a PLINK export plugin, and you can use PLINK/SEQ to convert that format to a VCF.

[Leonor Palmeira]

It's hard for me to get access to a computer running GenomeStudio (old experiment), so I just wrote a quick python script. Thanks a lot for your answer!

[Leonor Palmeira]

Thanks a lot for your help. I finally gained access to GenomeStudio and installed the PLINK export plugin. I then used PLINK/SEQ to convert to VCF. The details for all the steps necessary to do so, can be found here.

Answer 2

[jmzeng1314]

it's extremely easy for me to compare a genotyping data file with a vcf file.

The problem for me is how to get the genotyping data according to the IDAT files(red and green)

Answer 3

[dylkot]

As far as I can tell the pipeline described above is the main way to do this: GenomeStudio --(PLINK plugin)--> PLINK .ped file --(PLINK to vcf function)--> VCF. My only complaint about it is that PLINK swaps the allele order so that A2 is always major and so it won't preserve REF/ALT information. If you care about this (e.g. because you want to impute untyped variants) this means you need to identify the variants for which allele A2 does not match the reference and swap those alleles.

[ksuasteguic]

Hi, dylkot. Do you have any reference about how to do this? I would really appreciate it.