Special notes upgrading to Genomics Workbench 7.5

This section is a special note on upgrading to CLC Genomics Workbench 7.5 and CLC Genomics Server 6.5. This is intended for those upgrading from earlier versions and will provide information about how this change affects both existing and new data.

With the new version we have introduced three new variant callers: "Basic Variant Detection", "Fixed Ploidy Variant Detection", and "Low Frequency Variant Detection" (see Variant Detectors - overview). The Basic Variant Detection and Fixed Ploidy Variant Detection are similar in nature to the Quality-based and Probabilistic Variant Detection tools respectively. The main difference is that all filters, previously employed in either the Quality-based or Probabilistic Variant Detector, are now available in all three variant callers, in addition to a new filter: the relative read direction filter. The changes relating to the filters have some few consequences, and care must be taken when attempting to run the new variant callers with parameters that are equivalent to those used in the old ones (see figure 27.49) for details about the Fixed Ploidy Variant Detection and figure 27.48 for details about the Basic Variant Detection).

In particular:

The table shown in figure 27.48 contains a comparison of the Basic Variant Detection tool with the Quality-based Variant Detection tool, whereas the table in figure 27.49 shows a comparison of the Fixed Ploidy Variant Detection tool with the Probabilistic Variant Detection tool.

Image basic_variant_detection_comparison_table
Figure 27.48: Comparison of the Basic Variant Detection tool with the Quality-based Variant Detection tool.

Image fixed_ploidy_comparison_table
Figure 27.49: Comparison of the Fixed Ploidy Variant Detection tool with the Probabilistic Variant Detection tool.