A general question. What is the best package for genotype and CNV calling for beadchip 550k array?
I have check genomestudio from illumina, but it seems to only have windows version.
R/Bioconductor has a 550K annotation package that can be used with the crlmm package.
Thanks. What is the best QC practice?
For Affy SNP6, before CRLMM, I can do apt-geno-qc to filter for Constrast QC before calling. How about Illumina?