Shimmer is a program designed to identify somatic changes when run on two BAM files,
one from normal tissue and the other from a tumor sample. It uses Fisher’s exact test
along with multiple testing correction (Benjamini-Hochberg) to find significant
differences between allele composition with a specified false discovery rate.
Shimmer was written by Nancy Fisher Hansen, a staff scientist in the Genome Technology
Branch (GTB) of NHGRI, an institute at the National Institutes of Health. Nancy can be
reached at email@example.com.
- samtools 0.1.16 or above
- R 1.6.1 or above
- R “statmod” package (http://cran.r-project.org/web/packages/statmod/index.html)
Clone the Shimmer repository
git clone git://github.com/nhansen/Shimmer.git
cd Shimmer perl Build.PL ./Build ./Build test ./Build install
* For local installation, call perl Build.PL with “—install_base $HOME”