Question: Get Genotypes From Affymetrix Snp 6.0 Array
gravatar for pmoney1
7.9 years ago by
pmoney180 wrote:


Is there a pipeline/pacakage that can easily get me genotypes (eg in AA, AG, GG) type format from Affy genome wide SNP CEL files. Thus far I've played around with Birdseed and CLRMM. Both suffer from a combination of being impossible to install, having awful documention or producing unusable output. I literally want, CEL files go in, (annotated!!!!) genotypes and confidence scores come out. Any suggestions?

affymetrix snp genotype • 6.3k views
ADD COMMENTlink modified 12 months ago by freeseek100 • written 7.9 years ago by pmoney180

It helps to be more specific when describing problems. CRLMM is certainly not impossible to install, I have it on several machines. What difficulty are you having? What error messages? If impossible to install, how are you seeing output - and what makes you describe it as unusable?

You're also being unrealistic if you want a simple, black box solution: some work on your part is always required, regardless of the software. I suggest you take a deep breath, put your frustrations to one side and try describing the problem more clearly.

ADD REPLYlink written 7.9 years ago by Neilfws49k

CLRMM was actually okay to install, but it doesn't seem to produce annotated output. Or at least, it doesn't seem obvious how to do so. apt-probeset-genotype also doesn't seem to produce annotated output. I'd be pretty surprised if there wasn't a piece of software somewhere that gave you the actually SNP names and genotypes. The idea of having to write a script that manually parses the Affy annotation files is a bit ridiculous. The tone of my post may not have been great, but this has literally been driving me insane with frustration.

P.S. I want to use the genotypes in GenABEL (one of the few bioinformatics packages that actually has excellent documentation!!).

ADD REPLYlink modified 7.9 years ago • written 7.9 years ago by pmoney180
gravatar for Irsan
7.9 years ago by
Irsan7.2k wrote:

Edit by Kevin Blighe on March 10, 2020: Affymetrix was subsequently acquired by ThermoFisher, and the Genotyping Console can now be downloaded from HERE.


Affymetrix genotyping console

For SNP 6 it supports

  • calling genotypes
  • copy number/LOH
  • copy segments data
  • copy number variation analysis

Also see manual

ADD COMMENTlink modified 10 months ago by Kevin Blighe69k • written 7.9 years ago by Irsan7.2k
gravatar for freeseek
12 months ago by
freeseek100 wrote:

You can use the affy2vcf bcftools plugin. You will only need to run the apt-probeset-genotype software from APT, which is fast. Then you can easily convert the TXT output to VCF with both genotypes and confidence scores

ADD COMMENTlink written 12 months ago by freeseek100

Thanks for developing this, Giulio.

ADD REPLYlink written 10 months ago by Kevin Blighe69k
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