Changes

The initial set of genotype calls is generated examining a single individual at a time. These calls are typically quite good for deep sequencing data, but much less accurate for low pass sequence data. In either case, they can be greatly improved by models that combine information across sites and individuals and consider the contraints imposed by parent-offspring trios.  

The initial set of genotype calls is generated examining a single individual at a time. These calls are typically quite good for deep sequencing data, but much less accurate for low pass sequence data. In either case, they can be greatly improved by models that combine information across sites and individuals and consider the contraints imposed by parent-offspring trios.  

Note: The current version only supports SNP data, so please filter indels before running TrioCaller. It supports VCF 4.0 and 4.1 formats with the exception of dropped missing trailing fields (e.g. use complete missing notation ./.:.:.:.,.,. rather than ./. for the genotype field)

Note: The current version only supports SNP data, so please '''filter indels''' before running TrioCaller. It supports VCF 4.0 and 4.1 formats with the '''exception of dropped missing trailing fields''' (e.g. use complete missing notation ./.:.:.:.,.,. rather than ./. for the genotype field)

 

Here is a summary of the TrioCaller command line options (these are also listed whenever you run the program with no parameters):

Here is a summary of the TrioCaller command line options (these are also listed whenever you run the program with no parameters):