Recently I've been using the facets package for detecting CNVs in tumour-normal sample pairs. I think facets works great but facets being a collection of R functions (plus an external program to prepare the input), it requires manual interaction from the user and so it doesn't play well with a streamlined analysis pipeline.
cnv_facets wraps all the required steps, from BAM files to VCF output and summary plots, in a simple command line call:
cnv_facets.R -t tumor.bam -n normal.bam -vcf snps.vcf.gz -o tex
Installation can be done under regular user permission (no admin rights required) as:
git clone https://github.com/wwcrc/cnv_facets.git cd cnv_facets bash setup.sh /dir/on/your/path
For more information, check out the README file. Feel free to use and report any bugs, comments, questions.