Known Issues¶
All known issues with a fix version have been resolved in the specified release.
| Issue | Fix Version |
|---|---|
| Cases with low resolution BAF plots post cDSS 6.11.0 release have missing data | 6.11.1 |
| Recurrent or non-pass germline CNVs are not shown with the correct colour in the absolute allele count and low resolution BAF plots | 6.11.1 |
| There are minor discrepancies in the whole genome coverage values in cDSS and HTML | TBC |
| The total variant counts are discrepant in cDSS and HTML | TBC |
| Cancer Hotspots are not yet available for splice variants or Indels | TBC |
| Tooltip for QC flag column name and values in the germline small variant list is not visible | TBC |
| Clicking on an empty region of the SV chart removes all results from the corresponding variant list | TBC |
| The value for paired or split reads shows as 'Not applicable' for SVs with no SR/PR support | TBC |
| Population frequencies from the GnomAD genome studies are displayed on the variant list and variant details page, while the cancer HTML report uses the GnomAD Exome studies | TBC |
| Gene mode of action is missing in the gene track tooltip on the interactive plots available in somatic SV and CNV variant list page | TBC |
| Origin field not applicable for CNVs because the current pipeline uses Dragen's somatic CNV detection model, which does not strictly perform germline substraction of CNVs | TBC |
| Incorrect tooltip is shown for Paired reads and Supporting reads per billion in the variant details page | TBC |
| Following the NGIS Petra release H3C3, RXRA, SOS1, and YAP1 genes will not be labelled in the DSS with a mode of action or be flagged as being present in CGC when compared with the HTML report. | TBC |
| RefSeq transcripts are not visible in the somatic SV and CNV details page | TBC |
| High resolution BAF plots fail to load when the duplicate tab feature of some browsers is used | TBC |
| Publication date of the NGTD file used is missing in the variant lists and detail pages of some cases (please see the latest version of the Cancer Genome Analysis guide for further details). | TBC |
| Tumour structural variants plot shows CNVs when domain filters are removed | TBC |
| Legends of the coverage and high resolution BAF plots show information that applies only to the visualisation of older versions of the coverage and BAF plots | TBC |
| Legends of the germline BAF and absolute allele count plots show information that applies only to the tumour BAF and absolute allele count plots | TBC |
| chrX and chrY share same grey background in all plots available in the somatic SV and CNV variant list | TBC |
Warning
Following the NGIS Petra release, H3C3, RXRA, SOS1, and YAP1 genes will not be labelled in the DSS with a mode of action or be flagged as being present in CGC when compared with the HTML report due to a version difference. However, these genes will still show the correct domain. This discrepancy between the HTML report and the DSS is expected to be fixed in an upcoming release.
Dragen Cases
All cases processed by Dragen v4 (NGIS release Orion) should have the following case disclaimer in the cDSS, however it is currently not shown. This will be fixed in a future release. "The overall ploidy for this sample is estimated to be
Tumour First Cases
Variant filtering for reported variants in tumour first cases in the cDSS may differ from that in HTMLs: in these cases, we apply both somatic and germline prioritisation algorithms to all variants with GEL internal population germline allele frequency under 2%, so all such variants will appear on the cDSS. In the HTMLs and CSV tables, all variants with either GEL internal or gnomAD population germline allele frequency over 1% and no potential effect on cancer predisposition genes (nothing in the "Interpretation as germline" field) are filtered out. We are currently working on fully harmonising the variant lists between cDSS and HTML, and this discrepancy should disappear soon.
Copy Number Variant Coverage Plots
We have identified a bug in our plot generation, where genomic sex is being used rather than reported sex. If a cases genomic sex differs from the reported sex, the "expected coverage" line across chrX would display incorrectly. For further information and an example, see the "Tumour Copy Number Variant Plots" section in Visualisations.
Variant List Searching
We have identified a bug when searching the variant list. If a search is performed for a gene e.g., "TGFBR3" and selected from the search box dropdown, then the search bar is cleared and the same gene is searched for again i.e., "TGFBR3", the gene will not display in the search box dropdown a second time. The gene will still display in the variant list when entered into the search bar. Please see the video below illustrates the issue. For further information and an example, see the "Searching" section in Somatic Small, Germline Small or Somatic Structural and Copy Number variant list documentation.
Cancer loci files
At the time of the ‘Nembus’ release on the 9th October, 6 new loci were added used to annotate additional upstream/downstream variant data for cancer cases. These new loci were not included in cancer DSS. These variants are still visible and reported in the correct domain in cDSS, but they are not specifically annotated as being associated with the 6 new loci, which can still be visualised in IGV or the HTML report. The bug has been fixed as of the 6.4.1 release (13/11/2024) and any cases arriving to the cDSS from this point onwards will be unaffected. If you are interested in these loci and the case arrived to the cDSS between 9/10/2024 and 13/11/2024, please check the HTML report and IGV.
| Loci | chr | start | end |
|---|---|---|---|
| TAL1_upstream | 1 | 47232226 | 47242255 |
| TLX3_upstream | 5 | 171205524 | 171265681 |
| TLX3_downstream | 5 | 171312140 | 171349100 |
| ABL1_upstream | 9 | 130708042 | 130713015 |
| CRLF2_upstream | X | 1212650 | 1217650 |
| BCL11B_enhancer | 14 | 97382000 | 98876000 |
Please report any bugs or issues with the DSS via the Genomics England Service Desk.