Shimmer

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 nhansen@mail.nih.gov.

Build Dependencies

• git
• 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)

Build Instructions

Clone the Shimmer repository

git clone git://github.com/nhansen/Shimmer.git

Build Shimmer

cd Shimmer
perl Build.PL
./Build
./Build test
./Build install

* For local installation, call perl Build.PL with “—install_base $HOME”