Software / Pipeline For Affymetrix Genome-Wide Human Snp Array 6.0

Question

[pmoney1]

Hi,

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.

[donny.dw]

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?

Thanks

Answer 1

[Alex Paciorkowski]

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