tumor sample SNP6 copy number calling

Question

[Zhenyu Zhang]

Hi,

We are planing to call copy numbers from SNP6 array from tumor and normal samples. I know there are many tools normal sample genotyping. However, what's the best practice for tumor sample CNA calling?

Btw, I know that TCGA used GenePattern workflow from Broad. Broad also have some other tools such as birdsuite.