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Selection of Among samples (in the absence of sample attributes or when Paired analysis is not selected) utilizes information from all samples in the project in a joint variant detection. Against reference typically performs well when samples have good coverage and may contain unique SNPs. In instances where there is low coverage, Among samples may perform well for identifying SNPs shared between samples (but not for unique SNPs).

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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 in the drop-down list. Assemblies previously added to library files (see Library File Management) will be available for selection or New assembly… can be utilized to import the reference sequence to library files from within the task.

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References

1. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinforma Oxf Engl. 2009;25(16):2078-2079.
2. Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27(21):2987-2993.
3. Li H. Improving SNP discovery by base alignment quality. Bioinformatics. 2011;27(8):1157-1158.
   
   

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