I observed that VisualizeCnvs did not produce RD plots of all the variants meeting the size and type specifications. After tracing the workflow, it appears that RdTest does not plot records for which all samples are carriers. It records this in the metrics file output as All_samples_called_CNV_no_analysis, but we do not keep this file output in the workflow, so there is currently no log of the variant being dropped. We should determine the appropriate behavior so that either all variants are plotted, or those that are dropped are clearly recorded.
I observed that VisualizeCnvs did not produce RD plots of all the variants meeting the size and type specifications. After tracing the workflow, it appears that RdTest does not plot records for which all samples are carriers. It records this in the metrics file output as
All_samples_called_CNV_no_analysis, but we do not keep this file output in the workflow, so there is currently no log of the variant being dropped. We should determine the appropriate behavior so that either all variants are plotted, or those that are dropped are clearly recorded.