I am currently trying to analyse the presence of CNVs in a targeted sequencing dataset generated from Ion Torrent platform. The data description is as follows.
- Targeted region is a segment of the genome that spans multiple genes (not limited to exons).
- Single end reads of variable length.
- Reads are mapped to the hg19 assembly.
- The sample are not paired. We have a set of test and control samples.
So far, I have tried analysis using various tools such as CNVkit, CNVSeq, freec, codex. None of them seem to work well with the kind of data that I have in hand.
Can anyone suggest an analysis strategy that I could try with such data?