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?
- Genotype Calling (CRLMM) R package. Some vignettes were not updated since 2012.
- Genepatten: copy number pipeline. Unfortunately, that pipeline is currently non-functional due to a fire in data center in June, 2018.
- dchip (windows). The software is not maintained for years.
- Analysis Power Tools+PennCNV. This may be the best one now.
And do I need check cryptic relatedness between cases?