A very popular variant detection approach that performs well in many situations, Freebayes FreeBayes (version 1.0.1) employs a Bayesian statistical framework to determine the most likely combination of genotypes for the population in the sample(s) at each position in a reference genome for any number of individuals from a population.  It It is haplotype-based, calling variants based on the literal sequences of reads aligned to a particular target and not their precise alignment.  This This method can identify both single nucleotide variants and insertions/deletionsdeletion events.   Information on the model underlying the variant detection are detailed by Garrison et al.¹

FreeBayes dialog

Selecting Freebayes FreeBayes from the context sensitive menu will bring up the Freebayes task dialog (Figure 1), which contains two sections: Select Reference sequence and Advanced options.

Select Reference sequence will  will specify the reference assembly to utilize for variant detection.   If the alignment was generated in Partek^® Flow Flow^®, the the Assembly will  will be displayed as text in the section, and you do not have the option to change the reference.   In the event that alignment was performed outside of Partek^® Flow^®Partek Flow, you will need to select the appropriate Assembly utilized for alignment in the drop-down list. Assemblies previously added to library files (see see Library File Management) will be available for selection or or New assembly… in the menu can  can be utilized to import the reference sequence to library files from within the task.

Advanced options provides a means to tune parameters in the variant detection for optimal performance.   Upon invoking the task dialog, Option set is set to Default, and these parameters are provided by the Freebayes FreeBayes developers.   Clicking Configure button will open a window to tune advanced options (Figure 2).   Freebayes has advanced options for Population model, Allele scope, Indel realignment, Input filters, Mappability priors, Genotype likelihoods, Algorithmic features, and Report options.   Moving the mouse cursor over the info button will provide details for each parameter.   Please refer to the Freebayes FreeBayes documentation for further suggestions information on tuning these parameters.

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References

1. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. July 2012. https://arxiv.org/abs/1207.3907. Accessed October 3, 2016.