After reading this question, I downloaded the VarScan program, but have some questions about how to use it.
I have 10 Samples, 2 from each patient, one tumor, one normal The data is from a Solid 4 sequencer, and is single end reads, 50BP in length.
So, it seems to be possible to get CNVs using the varscan copyCaller. But how to use it?
java -jar VarScan.v2.2.5.jar copyCaller -h prints:
USAGE: VarScan copyCaller [output.copynumber] OPTIONS OPTIONS: --regions-file A list of regions (e.g. exons) to use for segmentation --output-file Output file to contain the calls --min-coverage Minimum read depth at a position to make a call  --min-region-size Minimum size (in bases) for a region to be counted 
I am really not sure about the syntax and the input.
- What is the input? Bam files? pileup files? Another format? If so, how does it look?
- How do I use it? e.g.
varscan copycaller normal.bam tumor.bam output.bam? (or same with pileup?)
- Or is there any other "workflow", maybe pre and post analysis/steps?