What are the popular tools to analyze the SNP & CNV from Genome-Wide Human SNP Array 6.0 data?

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Antonio Gomez

If you know R and how to use it, is better for you that take a look at Bioconductor and see the packages to deal with this kind of data. There are several

Waleed H. O. Aamer

I think you may be more specific by stating what type of studies you are doing ! That is because family based studies are different from population based ones. If you are studying a Mendelian trait and planning to do linkage analysis then I recommend using Merlin as it is very powerful in handling such huge data. However If you are studying a complex phenotype I think PLINK is very useful in this case.

Lalit Kaurani

Plink for SNP data n PennCNV for cnv data.

Bert Eussen

Look at Nexus Copy Number Biodiscovery for CNV detection if you have a small data set. < 2000