README.textile

h1. Shimmer

p. 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.

p. 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.

h2. 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)

h2. Build Instructions

h3. Clone the Shimmer repository

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

h3. Build Shimmer

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

p. * For local installation, call perl Build.PL with "--install_base $HOME"