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SubtitleText Selecting a variant detection method in the Partek Genotype Likelihood dialog AnchorName PartekVarDetectiondailog

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 score, a high log-odds score 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 default minimum log-odds on the reported SVN is 5. To change the value, click on Configure the Advanced options (Figure 2):

 

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SubtitleText Advanced options in Partek genotype likelihood variant detection method AnchorName PartekVarAdv

We recommend to check the Skip long reads option, which will ignore reads that span more than 0.1% of the reference.

Variant detection among sample option is to compare base composition across all the samples in the input data node, but not to compare the reference sequence. A high log-odds score indicates a strong chance that at  least one of the samples has a different base call at the position. This is useful in detection somatic mutations if there are 1 pair (two samples) in the input data. 

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