Changes

* The program '''polymutt''' implemented a likelihood-based framework for calling '''single nucleotide variants''' and detecting '''''de novo''''' '''point mutation''' events in families for next-generation sequencing data.  

* The program '''polymutt''' implemented a likelihood-based framework for calling '''single nucleotide variants''' and detecting '''''de novo''''' '''point mutation''' events in families for next-generation sequencing data.  

* The program takes as input genotype likelihood format (GLF) files which can be generated following the  [[#Creation of GLF files | Creation of GLF files]] instruction and outputs the result in the [[http://www.1000genomes.org/node/101 VCF]] format. For variant calling, alternatively polymutt can also take the VCF format input in which either the PL or the GL field are present. Commonly used variant calling algorithms such as GATK and samtools by default generate PL values in the VCF files. Current version works only on biallelic variants and non-biallelic variants in the VCF files will be ignored.

* The program takes as input genotype likelihood format (GLF) files which can be generated following the  [[#Creation of GLF files | Creation of GLF files]] instruction and outputs the result in the [[http://www.1000genomes.org/node/101 VCF]] format. Alternatively polymutt can also take the VCF format input in which either the PL or the GL field are present. Commonly used variant calling algorithms such as GATK and samtools by default generate PL values in the VCF files. Current version works only on biallelic variants and non-biallelic variants in the VCF files will be ignored.

* The variant calling and ''de novo'' mutation detection are modeled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops.

* The variant calling and ''de novo'' mutation detection are modeled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops.