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  • Here, we present a program, FamSeq, which reduces both false positive and false negative rates by incorporating the pedigree information from the Mendelian genetic model into variant calling. To accommodate variations in data complexity, FamSeq consists of four distinct implementations of the Mendelian genetic model: the Bayesian network algorithm, a graphics processing unit version of the Bayesian network algorithm, the Elston-Stewart algorithm and the Markov chain Monte Carlo algorithm. We developed a software package, FamSeq, which calls variants for family-based sequencing data. FamSeq is a free software package under GNU license (GPL v3), which can be downloaded from our website: http://bioinformatics.mdanderson.org/main/FamSeq, or from SourceForge: http://sourceforge.net/projects/famseq/.
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