CNV calling for illumina 550k array

Question

[Zhenyu Zhang]

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.

Answer 1

[Neilfws]

R/Bioconductor has a 550K annotation package that can be used with the crlmm package.

[Zhenyu Zhang]

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?