Help with de novo CNV analysis from GWAS data.

[pathaka001]

Hi,

I’m looking for de novo CNV changes a child (with cancer) of two normal adults. I've tried PennCNV for this with some success and am wondering if anyone out there has experience with other software like minimum distance (R bioconductor). Any suggestions are appreciated.

Thanks,
Anand

[severin]

Are you starting with Illumina reads? Have you thought about GATK haplotype caller? How big do you expect the CNV to be?