BardCNV

BardCNV is a program designed to identify copy number alterations when run on two BAM files for two different samples from the same individual.  BardCNV models read counts from the two alleles of heterozygous SNP sites in both the altered and unaltered samples to infer copy number changes using a hidden Markov model (HMM).

BardCNV 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

Build Instructions

Clone the BardCNV repository:

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

Build BardCNV:

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

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