Question: Software / Pipeline For Affymetrix Genome-Wide Human Snp Array 6.0
gravatar for pmoney1
7.9 years ago by
pmoney180 wrote:


I'm wondering if anyone can recommend any software / pipeline for analysing Affymetrix Genome-Wide Human SNP Array 6.0. Preferrably something that does an integrative analysis of the SNP and CNV data. I tried using "Birdsuite" but gave up after about 6 hours of trying to install it.

affymetrix snp • 3.6k views
ADD COMMENTlink modified 7 months ago by donny.dw10 • written 7.9 years ago by pmoney180

I have the same question after 7.3 years,

what is the best pipeline to analyze affymetrix snp 6.0 array in 2020?

I found there are several options, could you please give me some suggestions which one is the best and is there any other option?

  1. Genotype Calling (CRLMM) R package. Some vignettes were not updated since 2012.
  2. Genepatten copy number pipeline in Genepattern. Unfortunately, that pipeline is currently non-functional due to a fire in data center in June, 2018.
  3. PennCNV.
  4. dchip (windows). The software is not maintained for years.

And do I need check cryptic relatedness between cases?


ADD REPLYlink written 7 months ago by donny.dw10
gravatar for Alex Paciorkowski
7.9 years ago by
Rochester, NY USA
Alex Paciorkowski3.4k wrote:

You can use PennCNV. Here's a tutorial. Or if you want to spend a lot of money you can use Nexus.

ADD COMMENTlink written 7.9 years ago by Alex Paciorkowski3.4k
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