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* The current version performs variant calling and ''de novo'' mutation detection from files in the genotype likelihood format (GLF). In future versions we plan to take [[http://samtools.sourceforge.net/ SAM/BAM]] files as input. See the following for instructions on how to create GLF files.
* The current version performs variant calling and ''de novo'' mutation detection from files in the genotype likelihood format (GLF). In future versions we plan to take [[http://samtools.sourceforge.net/ SAM/BAM]] files as input. See the following for instructions on how to create GLF files.
** Download a modified version of samtools ( [[https://github.com/statgen/samtools-0.1.7a-hybrid samtools-hybrid]] )
** Download a [[Samtools-hybrid|modified version of samtools]] ( [[https://github.com/statgen/samtools-0.1.7a-hybrid samtools-hybrid]] )
** Prepare the reference genome in fasta format and sequence alignments in [[http://samtools.sourceforge.net/ SAM/BAM]] format
** Prepare the reference genome in fasta format and sequence alignments in [[http://samtools.sourceforge.net/ SAM/BAM]] format
** Generate BAQ adjusted GLF files using the following command
** Generate BAQ adjusted GLF files using the following command
