Changes

== Introduction ==

== Introduction ==

* The program '''bayesdenovo''' implemented a Bayesian framework for calling '''''de novo''''' mutations in '''nuclear families''' (including trios, quartets, and families with more siblings) for next-generation sequencing data.  

* The program '''bayesdenovo''' implemented a Bayesian framework for calling '''''de novo''''' mutations in '''nuclear families''' (including trios, quartets, and families with more siblings) for next-generation sequencing data. If infers Identity-by-Descednt (IBD) allele sharing to increase the '''''de novo''''' mutation calling accuracy. As a result, the IBD sharing for the called '''''de novo''''' mutations is also available in the output file.

* It takes as input a standard VCF file with PL or GL fields (storing genotype likelihoods). Commonly used callers, e.g. GATK and samtools, generate VCF files with PL values.

* It takes as input a standard VCF file with PL or GL fields (storing genotype likelihoods). Commonly used callers, e.g. GATK and samtools, generate VCF files with PL values.

* It calculates the likelihood of the model with '''''de novo''''' mutations, denoted as L1, and the likelihood of Mendelian transmission, denoted as L0, and represent the '''''de novo''''' evidence using a Bayesian factor BF=L1/L0. In TrioDeNovo the  '''''de novo'''''  quality is represented as DQ=log10(BF) = log10(L1/L0).

* It calculates the likelihood of the model with '''''de novo''''' mutations, denoted as L1, and the likelihood of Mendelian transmission, denoted as L0, and represent the '''''de novo''''' evidence using a Bayesian factor BF=L1/L0. In TrioDeNovo the  '''''de novo'''''  quality is represented as DQ=log10(BF) = log10(L1/L0).