Deriving Illumina genotypes from LRR and BAF data

Question

[alexandre.caetano]

Hi all. Anyone knows a robust method to obtain genotypes from Illumina LRR and BAF data? Any pointers will be greatly appreciated. Cheers

[Kevin Blighe]

If you have managed to obtain the LRR and the BAF, then you should also have the genotype, as these are all produced together by programs like, for example, PennCNV.

You could try to infer the genotype from the LRR and BAF, but you would still need to know the SNPs that are genotyped at each and every position.

The most important question: from where did you obtain the data?