Get Genotypes From Affymetrix Snp 6.0 Array

Question

[pmoney1]

Hi,

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?

[Neilfws]

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.

[pmoney1]

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!!).

Answer 1

[Irsan]

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

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Affymetrix genotyping console

For SNP 6 it supports

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

Also see manual

Answer 2

[Giulio Genovese]

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

[Kevin Blighe]

Thanks for developing this, Giulio.