Hi
I am the developer of
CNAnorm which is designed for normalisation, segmentation, GC correction and plotting of copy number data from very low coverage (~ 0.05X) whole genome sequencing. It also works with higher coverage (obviously takes more time and you will need a few tweeks) and some report using it sucesfully on exome capture data.
Please read
this post where other users posted their questions and I provided some suggestions.
good luck