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The Quality section of the filter task will involves metrics generated from the variant detection, and these will be dependent upon the method utilized for variant detection.   Moving the mouse cursor over the info button will provide details for each parameter.  Decisions on quality filtering parameters should be based upon sequencing assay design as well as goal or the study, either identification of all potential variants or identification of high confidence variants.  At the very least, the use of Minimum read depth should be considered for filtering to ensure sufficient read evidence was available to call a variant.  In instances where paired variant detection was performed in Samtools, Minimum genotype log ratio may be employed to ensure sufficient evidence of genotype differences in case and control sample pairs.  Please refer to the Samtools, FreeBayes, and LoFreq documentation for further details on any of these parameters.

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