The 5.x release line is the final line of the Biomedical Genomics Workbench. From November 28, 2018 biomedical genomics analysis and panel data analysis functionality will be delivered through the QIAGEN CLC Genomics Workbench, QIAGEN CLC Genomics Server, and the free plugin – Biomedical Genomics Analysis.
- Fixed a bug where the “Unaligned end” field provided in the Breakpoint track output of the Indel and Structural Variants tool was left blank when the value should have been “Mixed consensus” on all but one chromosome. The field is now filled for all chromosomes.
- Fixed a issue with the Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools that caused a small minority of variants to go unreported under certain conditions expected to arise rarely.
- Fixed an issue affecting the Map Reads to Reference tool when it was included in a workflow, where if the References parameter was connected to an input, and a masking track was configured, an error was reported stating that the masking track was incompatible with the reference genome, whether or not it was compatible.
- Fixed a concurrency bug in the Copy Number Variant Detection tool, which very rarely resulted in the tool reporting all low-coverage targets on one or more chromosomes as false positive deletions.
- Fixed error thus MRNA_LIKE tracks can be seen in the select file dialogue when creating custom reference dataset.
- Fixed a bug in the Identify Candidate Variants tool where no results were returned when one or more criteria used a comparison operator with more than one term (e.g. “>=”, “abs value <“).
- Fixed the links to the AmiGO Gene Ontology website used for GO annotations.
- Fixed a bug where in some cases, the Search for Reads in SRA… tool would not fetch the final page of results.
- Various minor bugfixes.
- SOLiD colorspace data support, including import, is not available in the the next major release line of the software.
- Roche 454 NGS import is now a legacy tool. We have retained it in the next major release line of the software, but it may be retired in a future release.
If you are concerned about these changes, please contact the QIAGEN Bioinformatics Support team (firstname.lastname@example.org).