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

FreeBayes dialog

Selecting 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 specify the reference assembly to utilize for variant detection.  If the alignment was generated in Partek^® Flow^®, the Assembly 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^®, you will need to select the appropriate Assembly utilized for alignment. Assemblies previously added to library files (see Library File Management) will be available for selection or New assembly… in the menu can be utilized to import the reference sequence to library files 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 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 documentation for further suggestions on tuning these parameters.

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.

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