Changes

=== Genotype Refinement Using Linkage Disequilibrium Information (TrioCaller) ===

=== Genotype Refinement Using Linkage Disequilibrium Information (TrioCaller) ===

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 the contraints 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.  

The following parameters are available.  Ones with "[]" need specification:

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

Available Options

Available Options

   Shotgun Sequences: --shotgun [], --pedfile []  

   Shotgun Sequences: --shotgun [], --pedfile []  

Explanation of Options

Explanation of Options

             --shotgun:   Standard   [http://www.1000genomes.org/node/101 VCF file (4.0 and above)] .         

             --shotgun:   Standard [http://www.1000genomes.org/node/101 VCF file (4.0 and above)] .         

             --pedfile:    Pedigree file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html MERLIN format].

             --pedfile:    Pedigree file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html MERLIN format].

                 --seed:    Seed for sampling, default 123456.

                 --seed:    Seed for sampling, default 123456.

           --errorRate:    The pre-defined base error rate. Default 0.01.

           --errorRate:    The pre-defined base error rate. Default 0.01.

         --randomPhase:    The initial haplotypes are inferred from the single marker. Default option.

         --randomPhase:    The initial haplotypes are inferred from the single marker. Default option.

         --inputPhased:   The initial haplotypes are directly from input VCF file (with "|" as separator in the genotype column).

         --inputPhased:   The initial haplotypes are directly from input VCF file (with "|" as separator in the genotype column).

           --refPhased:   The initial haplotypes are built on reference alleles from VCF file.

           --refPhased:   The initial haplotypes are built on reference alleles from VCF file.

               --prefix:    The prefix of output file   

               --prefix:    The prefix of output file   

     --interimInterval:    The number of rounds for interim outputs

     --interimInterval:    The number of rounds for interim outputs