excellent blog post showing how segmental duplications can skew ur CNV analysis & SNP calling. The latter was something I wasn't aware of ....
Alert followers of this blog may recall a cautionary statement I made
previously about working with Illumina CNV data — that males and
females sometimes have different baseline signal intensity levels (this
was more of a GenomeStudio software issue than a hardware problem).
To find out if this issue affects the Omni2.5, I ran a simple t-test to
compare the Log-R Ratio (LR) intensity values between males and
females across the genome. The results are shown in the Manhattan Plot