DeNovoGear is a tool to detect denovo mutations using sequencing data of related individuals. DeNovoGear calls denovo SNP's and INDEL's in trios. DeNovoGear can also be used to phase denovo mutations using genotype information at neighboring SNP sites. In addition, DeNovoGear can also be used to analyze a pair of samples and call SNP's and INDEL's present in one sample but not the other.
DeNovoGear is an open source program that can be downloaded from the SourceForge page here.