Special notes upgrading to Genomics Workbench 6.5

This section is a special note on upgrading to CLC Genomics Workbench 6.5 and CLC Genomics Server 5.5. 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, variants that are adjacent are reported as one variant (one row in the table view). Previously, if e.g. two adjacent SNVs were detected in the same reads, they would be reported as two variants (two separate rows), linked together in a linkage group. Each linkage group was given a namber and this number put in a column with the header 'linkage' in the variant track table. This caused a lot of confusion and interpretation problems for our users. Although we realize that changing the behavior of the variant callers will create disturbance in the analysis pipelines of our users, we have decided that we cannot ignore the feedback coming from a range of users reporting problems when interpreting the linked variants.

The change has a few consequences:

Please note that previously, linked variants would get one set of attributes, e.g. one count. When these variants are split either by the automatic conversion when creating a new track, or by the dedicated conversion plugin, each of the variants will inherit the attributes from the linked variant. In some cases, these values will be different from the values that would be calculated if the variants are calculated from scratch with the new version. As an example, the counts could be different when calculated separately for each variant compared to the count for the combined variant.

If it is important to ensure correct reporting of values for variants that were previously linked, we recommend rerunning the variant detection in the new version.