Question: CNV calling for illumina 550k array
0
gravatar for Zhenyu Zhang
4.6 years ago by
Zhenyu Zhang240
United States
Zhenyu Zhang240 wrote:

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.

 

ADD COMMENTlink modified 4.6 years ago by Neilfws48k • written 4.6 years ago by Zhenyu Zhang240
0
gravatar for Neilfws
4.6 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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

ADD COMMENTlink written 4.6 years ago by Neilfws48k

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? 

ADD REPLYlink written 4.6 years ago by Zhenyu Zhang240
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