TrioCaller

The program is based on a LD-aware method to infer genotypes and phasing for sequencing in trios (or mixed with undrelated individuals). 
A brief tutorial is given below. A more detailed version is on 
wiki page
weichen.mich@gmail.com  or  Goncalo Abecasis  goncalo@umich.edu

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The following parameters are available.  Ones with "[]" are in effect:

Available Options
   Shotgun Sequences : --shotgun [],--pedfile []
      Markov Sampler : --seed [123456], --burnin, --rounds [2]
          Haplotyper : --states, --errorRate [0.01], --compact
             Phasing : --randomPhase [ON], --inputPhased, --refPhased
        Output Files : --prefix [], --interimInterval
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Explanations of the some input parameters.


--shotgun
Standard VCF 4.0 file LINK
--pedfile
Pedigree file in MERLIN format LINK
--randomPhase
The initial haplotypes are inferred from the single marker
--inputPhased
The initial haplotypes are directly from input VCF file
--refPhased
The initial haplotypes are built on reference alleles from VCF file
--interimInterval
The number of rounds for interim outputs

An example:
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./TrioCaller --shotgun test.vcf --pedfile test.ped --states 50 --randomPhase --rounds 30 --prefix result

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Citation: Wei Chen, Bingshan Li, Serena Sanna, Carlo Sidore, Fabio Busonero, Yun Li and Goncalo Abecasis. Genotype Calling and Haplotyping In Parent-Offspring Trios (2011) Submitted