Flow Documentation

Partek Flow Documentation

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If the Log Odds are undefined because of machine numeric representation limitations, then the log odds are capped at 106.

Partek Genotype Likelihood Dialog

Selecting Partek Genotype Likelihood from the context sensitive menu will bring up the task dialog, which contains three default sections: Variant detection method, Select Reference sequence, and Advanced options.
In the Variant detection method drop-down list, Against reference will compare base composition for each sample against the reference sequence assembly, independently (Figure 1).  

 

 

Numbered figure captions
SubtitleTextSelecting a variant detection method in the Partek Genotype Likelihood dialog
AnchorNamePartekVarDetectiondailog

Image Added

The reference sequence assembly should be selected from the drop-down list if the first input data file in the pipeline is a bam file. If the first input data file is raw sequence file, and the data is aligned in Partek Flow, then the reference sequence assembly used here is the same as the one used in the alignment step, there is no need to select the reference sequence.

The detection method produce log-odds ratio, a high log-odds ratio for a reported SNV indicates a strong chance that the nucleotide is different from the reference sequence at that particular position in the detected sample.  By When Configure the Advanced options