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

Question

[donny.dw]

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. Unfortunately, that pipeline is currently non-functional due to a fire in data center in June, 2018.
3. dchip (windows). The software is not maintained for years.
4. Analysis Power Tools+PennCNV. This may be the best one now.

And do I need check cryptic relatedness between cases?

Thanks

Answer 1

[Kevin Blighe]

Hey, my own doctoral degree was based on samples profiled with this array. Indeed, many tools have entered the 'dust pile' for various reasons, and the merger between Affymetrix and ThermoFisher did and did not help.

Birdsuite (SNP and CN)

I cannot see beyond recommending Birdsuite for profiling both SNP and CN probes from this array, essentially following the methods employed by the TCGA consortium:

• https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/CNV_Pipeline/
• https://www.broadinstitute.org/birdsuite/birdsuite

Genotyping Console (SNP and CN)

You may still be able to use the Genotyping Console for calling SNPs (however, as I understand, their support team was essentially decommissioned due to the large merger with ThermoFisher, and is now being run by volunteers):

• A: Get Genotypes From Affymetrix Snp 6.0 Array

Aroma Affymetrix (CN)

Another project that provides functional packages is Aroma:

• https://www.aroma-project.org/

Kevin