HomeCLC software: Important notificationsIssues affecting only older versions of productsVariant calling on results from RNA-Seq Analysis cannot detect insertions and deletions at intron-exon boundaries

2.19. Variant calling on results from RNA-Seq Analysis cannot detect insertions and deletions at intron-exon boundaries

Issue description

Read mappings produced by the RNA-Seq Analysis tool treat deletions and insertions at exon-intron boundaries as splice variants. This means that such deletions/insertions are not detected in downstream variant calling.

 

Figure 1: An example of the issue as seen in CLC Genomics Workbench 11. The short deletion in the middle of the right-hand side exon, seen in the Read Mapping track, is found by the variant detection tools in the Workbench and appears in the variant track. However, the deletions at the end of the first exon and the start of the second exon are not identified by the variant detection tools, but rather are treated as if they were splice variants. In addition, the inserted sequence "GAAAA" is not detected.

 

This issue will be fixed in the forthcoming CLC Genomics Workbench 12 release, expected at the end of November, 2018. With that release, the data above would look like that shown in Figure 2, below.

Figure 2: The same data analyzed in the upcoming CLC Genomics Workbench 12. All deletions and insertions in the mapping can, in principle, be found by the variant detection tools, subject to the statistical model and settings used. This image shows the results of an analysis with very lax settings for illustration purposes. This corrected behavior implicitly favors the hypothesis of a deletion/insertion over a novel splice junction.

 

Affected software

  • CLC Genomics Workbench 11.x and earlier.
  • All versions of Biomedical Genomics Workbench.
  • CLC Genomics Server 10.x and earlier

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