MSG: Multiplexed Shotgun Genotyping http://genomics.princeton.edu/AndolfattoLab/MSG.html https://github.com/tinathu/msg http://www.ncbi.nlm.nih.gov/pubmed/21233398 ### Dependencies ### Python (2.6.4) bwa (0.5.7) samtools (0.1.9-3) biopython-1.53 Pyrex-0.9.9 pysam-0.1.2 (apply fix as described here: http://code.google.com/p/pysam/issues/detail?id=22&can=1&q=dandavison0) R packages (HiddenMarkov 1.3-1, zoo 1.6-2, R.methodsS3 1.2.0 and R.oo 1.7.3) ### Installation instructions ### git clone git@github.com:tinathu/msg.git cd msg make