I've got a batch of target sequencing data and I want to identify the CNV or LOH in Chr1 and Chr19, besides the chr1 and chr19 region, I also have some target regions which are used to call SNPs. Since my samples are all tumor samples, there is no paired normal sample, so I want to find some "stable" control genes and use them to identify that if the chr1 and chr19 regions possess gains or losses. Through the experiment, we have known that which sample has the chr1 and chr19 losses.
I have got all the read count numbers and read depth of each target region segments. If there is any good methods or algorithm that I can evaluate the stable regions and use them as control.
I have tried some CNV calling softwares, like cn.mops, but since my sequencing data among samples is unbalanced, and this may affect the outcome. It has lots of difference with our experiment outcome. Control-FREEC can not be used in target sequencing data without normal samples.
Any suggestions would be appreciated. Thank you for your time.