README.textile

h1. Bam2mpg

p. The program "bam2mpg" calls genotypes from sequence reads of haploid or diploid DNA aligned to a closely-related reference sequence. The program reads alignments in BAM format (http://samtools.sourceforge.net). The MPG (Most Probable Genotype) algorithm is based on a Bayesian model which simulates sampling from one or two alleles with sequencing error, and then calculates the likelihood of each possible genotype given the observed sequence data. Using prior probabilities dependent on the expected heterozygosity of the sequence, MPG then predicts the "Most Probable Genotype" at each site, along with quality scores estimating the accuracy of the calls.

p. Bam2mpg 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.

p. If you use bam2mpg in your work, please cite the paper: Teer, J.K. et al. 2010. Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Research. 20(10):1420-31.

h2. Build Dependencies

• git
• samtools 0.1.16 or above

h2. Build Instructions

h3. Clone the bam2mpg repository:

bc. git clone git://github.com/nhansen/bam2mpg.git

h3. Build bam2mpg:

bc.. cd bam2mpg perl Build.PL ./Build ./Build test ./Build install

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