Two reference insertion variants can be reported at the same position Issue description In regions where the evidence could support different insertions, it is possible for 2 reference variants to be reported at the insertion position, instead of one reference variant, as would be expected. If this effect is observed in your data, we recommend carefully inspecting the corresponding area of the read mapping to evaluate the reported variants. Two reference insertions at a given position will look something like this in a variant track: Affected software. CLC Genomics Workbench 7.5 and up. Biomedical Genomics Workbench 2.1 and up. CLC Genomics Server 6.5 and up 1.2. Reference multi-nucleotide variants (MNVs) are removed when applying filter or annotation tools under some circumstances Issue description In rare cases, reference MNVs may be removed in error by tools that add and remove information to variants, and tools that filter variants.
This occurs when an MNV is called as the reference allele for a region containing multiple SNVs, as opposed to the usual case where a reference MNV is called for a variant MNV. Expected impact This issue is expected to affect a minority of variants, arising where there is low support for a given variant. This is most likely in analyses where very low frequency variants are being considered. For example, the Identify QIAseq DNA Variants workflow provided by the QIAseq Targeted Panel Analysis plugin contains a Low Frequency Variant Detection step configured to call variants at a frequency of 1%. At such low frequencies, the chance of calling SNVs next to each other, while lacking the evidence needed to identify an MNV, increases, especially if the data is of low quality.
In this workflow, variant detection is followed by the 'Remove False Positives' tool, which will filter any reference MNV allele without a corresponding variant MNV. Further background In, if contiguous single nucleotide variants (SNVs) have been found, evidence is sought in the reads for the presence of an MNV. If this evidence exists, the contiguous SNVs are reported as an MNV. Otherwise, they remain classified as SNVs. During the, count and coverage filters are applied, and potential variants identified before this point will be filtered out if they do not meet the necessary cut-off criteria.
For a region with two or more contiguous, heterozygous SNVs in the data, it is possible for a potential variant MNV allele to be filtered out at this step such that the variants are represented as multiple SNVs, but for the reference MNV to not be filtered. Affected software. All versions of Biomedical Genomics Workbench. CLC Genomics Workbench 6 and up. CLC Genomics Server 5.0 and up 1.3. Loss of reference allele information for neighboring SNPs when using certain downstream filtering tools after variant calling An issue was discovered where (MNV) representing a reference allele would be filtered out when any of the filtering tools listed below was used. As a consequence of this problem, the number of reads reported as supporting the reference allele could be incorrect after filtering was carried out.
If the output was then exported, e.g. To VCF, the incorrect counts would also be exported. We expect the issue described here to have little or no impact on the identification or interpretation of variant calls within the Workbench. Software affected.
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From CLC Genomics Workbench 6.0.4 and up. All versions of Biomedical Genomics Workbench. From CLC Genomics Server 5.0.4 and up List of tools that cause the described behavior CLC Genomics Workbench Biomedical Genomics Workbench.
Annotate with Overlap Information. Annotate with Flanking Sequences. Annotate with Exon Numbers.
Compare Variants within Group. GO Enrichment Analysis. Add Information from Overlapping Genes. Add Flanking Sequences. Add Exon Numbers. Compare Shared Variants in a Group of Samples 2. Issues affecting only older versions of products.
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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 2.2. RNA-Seq Analysis does not count some reads covering start-end position of a circular chromosome A problem with read counts has been identified in the RNA-Seq Analysis tool when using circular reference sequences. It affects all single reads and some paired end reads that map across the start/end positions of a circular reference where there is a gene annotation over this region. Affected reads are mistakenly considered as mapping to an intergenic region. For affected analyses, all count values for the genes crossing the start/end position of the circular reference, as well as values with derivations depending on these counts, will be incorrect. This issue does not affect RNA-Seq analyses where the 'One reference sequence per transcript' option has been selected. It also does not affect analyses using the older legacy RNA-Seq Analysis tool.
Work around If your analyses are affected by this problem, the work around involves redefining the start point of circular references to lie outside a gene region and re-running the analyses with the new references. These are the standard steps that would be involved:.
Create a standard, annotated sequence or sequence list using the circular reference by using the Convert from Tracks tool, selecting the sequence track and all annotation tracks that you want to use for this or any other analysis involving these references. View the reference sequence to be adjusted in circular view and move the start position to somewhere not covered by a gene annotation. How to do this is describe in the manual at:.
Use the Convert to Tracks tool on the annotated reference sequence(s), choosing to generate a sequence track and all the annotation track types you originally chose when you converted to tracks. Please ensure the new references and annotation tracks are easily distinguished from the old ones. Using a mix of the new reference sequences with old annotation tracks, or vice versa, would cause incorrect results.
This is because the annotations would be in the wrong location along the reference sequence if a mix of the old and new reference tracks were used. Software affected. CLC Genomics Workbench 7.x, 8.x, 9.x, 10.x and 11.x. All versions of Biomedical Genomics Workbench. CLC Genomics Server 6.x, 7.x, 8.x, 9.x and 10.x 2.3. Some comparison operators in the Identify Candidate Variants tool do not work Issue description Comparisons involving the following operators in the Identify Candidate Variants tool do not work and produce empty results:.
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abs value =15 could be specified as x14 when filtering on integer values. Affected software. CLC Genomics Workbench 10.1, 10.1.1, 10.1.2, 10.1.3, 11.0 and 11.0.1. Biomedical Genomics Workbench 4.1, 4.1.1, 4.1.2, 4.1.3, 5.0 and 5.0.1. CLC Genomics Server 9.1, 9.1.1, 9.1.2, 9.1.3, 10.1and 10.0.1 This issue affects the Identify Candidate Variants tool, whether run directly or via a workflow. Ready-to-use workflows distributed with the Biomedical Genomics workbench or plugins that contain the Identify Candidate Variants tool are not affected as distributed, as the default configurations contain only working comparison operators. If such a workflow is copied, and an Identify Candidate Variants element is edited to include an affected operator, then the newly created workflow will be affected when run on the software versions listed above.
Variant calls possible within common sequence regions of QIAseq DNA panel results under specific circumstances Issue description For paired QIAseq panel data, common sequence is left on the end of the non-indexed read when that read is longer than the DNA fragment being sequenced. This will usually not cause problems, as the contaminating common sequence is not aligned to the reference by the read mapper, and so is ignored by variant detection tools. However, false positive variants may on occasion be called when i) enough of the common sequence, by chance, matches the reference, leading to alignment and ii) there is at least one mismatch in that region, leading to a variant call. We expect false positive variants in such regions to occur rarely in practice due to the combination of circumstances needed. See the Further Background section below for more information.
This issue is caused by a problem with the Remove Ligation Artifacts tool. This tool, and workflows that include this tool, are distributed in the QIAseq DNA V3 Panel Analysis and the QIAseq Targeted Panel Analysis plugins. A full list of software and versions affected is provided at the end of this article. Further background When the length of a sequencing read exceeds the length of the DNA fragment being sequenced, the read can end with artifacts from library preparation, such as adapter sequence. In the case of paired QIAseq V3 panel data, an artifact routinely encountered is 'common sequence' at the 3' end of the non-indexed read. This is shown in simplified form below. If the read is long enough, it may also contain some of the UMI sequence.
The Remove Ligation Artifacts tool trims away artifacts, so that they are not considered in variant detection analysis. However, in the affected software, regions of common sequence and UMI sequence remain on the non-indexed read of a pair. This is generally not a problem, as the common sequence and UMI do not usually match the reference where the read has mapped. Non-matching regions in read mappings are ignored when variant detection analysis is run. However, if the part of the common sequence adjacent to the DNA fragment, by chance, matches the reference well enough to be mapped, variant detection tools will consider that region.
At least 2 bases of the common sequence near the target region must match the reference for this to happen with default read mapping penalties. If such a region matches perfectly, then this does not affect the variant detection results as no variants will be reported. However, if at least one base does not match the reference, then a variant can potentially be called within the common sequence region. Examples A false positive variant, in the common sequence at the 5' end of the DNA fragment of interest: The CCT within the red box is part of the common sequence, but the 2 Cs happen to match the reference at this point. This leads to these bases being mapped to the reference and being considered during variant detection analysis. The T of the CCT does not match the reference, and here has been called as a variant by the variant detection tool. A false positive variant, in the common sequence at the 3' end of the DNA fragment of interest: The AGGA in the red box is part of the common sequence.Three of the four bases in this region happen to match the reference, so this region is mapped to the reference and is thus considered during variant detection analysis.
The first G in this region does not match the reference, and in this case is called as a variant by the variant detection tool. Other symptoms When considering if a particular variant is a false positive due to this issue, it can be useful to consider that the common sequence will appear on only one of the pair members - either only the ones that map in the reverse direction to the reference, OR only the ones that map in the forward direction to the reference. To check for this, choose the option in the Reads Track section of the side panel called 'Disconnect paired reads' and check if all the affected reads are red or all of them are green. Search for Sequences at NCBI tool missing first and last result An issue with the Search for Sequences at NCBI tool was introduced in Workbench products released on the March 2, 2017 where the first and last search result in each result page returned by the search was missing. For searches for a specific accession number, the outcome of this problem was that no result was listed, even though the 'Total number of hits' reported was 1. For searches with multiple results, the first and last entry on each page of results returned was missing. Software affected This issue was introduced in, and only affects:.
CLC Genomics Workbench 10.0. CLC Main Workbench 7.8. CLC Sequence Viewer 7.8 This issue was fixed in CLC Genomics Workbench 10.0.1, CLC Main Workbench 7.8.1 and CLC Sequence Viewer 7.8.1, released on March 15, 2017. Marginally higher counts reported for a small subset of variants The count and read count values reported by the Basic Variant Detection, Low Frequency Variant Detection and Fixed Ploidy Variant Detection tools were found to be marginally higher than was actually the case for a small minority of cases. We expect the issue described here to have little or no impact on the identification or interpretation of variant calls within the Workbench. The issue described here has been fixed for the. CLC Genomics Workbench 9.5.4.
Biomedical Genomics Workbench 3.5.4 and. CLC Genomics Server 8.5.4 These versions were released on February 14, 2017. Issue details This issue involves potential variants that overlap, where one of the overlapping variants, but not the other, is confirmed and reported as a variant in the results. The consequences of this issue are, for the small group of affected variants:.
Slightly higher variant frequencies could be reported than should have been. For some cases this could result in allele frequencies above 100% being reported.
Using software where this issue has been fixed could result in a small decrease in the final number of variants reported when compared to results reported using earlier versions. This would be due to some potential variants no longer passing the count, read count or allele frequency filtering constraints set.
To give an idea of the magnitude of the change that one might observe: in our tests, for a particular analysis that reported 250,000 variants, 30 fewer were reported with the same parameters and filters applied after the fix to this issue was implemented. Software affected. CLC Genomics Workbench 7.5 up to and including version 9.5.3. Biomedical Genomics Workbench 2.1 up to and including version 3.5.3. CLC Genomics Server 6.5 up to and including version 8.5.3 3.3. Coverages and read counts for variants in certain circumstances are incorrect The reporting of coverage, read coverage, read count and forward and reverse read count of the Basic Variant Detection, Fixed Ploidy Variant Detection and Low Frequency Variant Detection tools could be incorrect for variants meeting the particular conditions described below.
We expect the issues described here to have little or no impacton identification or interpretation of variant calls. The issues described here have been fixed for the. CLC Genomics Workbench 9.5.3. Biomedical Genomics Workbench 3.5.3 and. CLC Genomics Server 8.5.3 These versions were released on December 14, 2016. We expect the issues described here to have little or no impact on identification or interpretation of variant calls.
Issue description. For SNVs with no immediately adjacent variants, overlapping reads of a pair that had conflicting base calls for that variant position were contributing to the values calculated for coverage, read coverage, and read count of that variant. Such reads should not have contributed to these values.
For SNVs with no immediately adjacent variants, and where paired read data is used, if the second read of a pair containing the variant did not meet the requirements of the quality filter, neither the first nor second read of that pair were contributing to the coverage calculated for the variant. In such cases, if the first read did pass the quality filter, it should have contributed to the coverage calculation. For variants identified as adjacent to one or more other variants, the values for count, read count, and forward- and reverse read count could be incorrect for variants found in overlapping regions of a pair of reads. The coverage of a longer variant that contained another variant was being reported for both the longer variant and the contained variant. Software affected. CLC Genomics Workbench 7.5 up to and including version 9.5.2. Biomedical Genomics Workbench 2.1 up to and including version 3.5.2.
CLC Genomics Server 6.5 up to and including version 8.5.2 3.4. Simultaneously run RNA-Seq jobs using the EM option can fail or produce incorrect results on Workbenches The issue described below has been fixed for CLC Genomics Workbench 9.5.2 and Biomedical Genomics Workbench 3.5.2. If you are running the CLC Genomics Workbench 9.5.1 or 9.5, Biomedical Genomics Workbench 3.5.1 or 3.5, please update your installation. Issue description Using CLC Genomics Workbench 9.5.1 and 9.5 and Biomedical Genomics Workbench 3.5.1 and 3.5, RNA-Seq Analysis may fail or report wrong results if multiple instances of the RNA-Seq Analysis tool are run simultaneously with the EM option turned on. The following conditions are necessary before the issue can arise:.
RNA-Seq Analysis is run with the EM option turned on AND. Two or more such RNA-Seq Analysis tasks are run concurrently. This does not affect jobs run using the, or jobs run on a CLC Genomics Server. Actions to take Upgrade your Workbench to the latest version.
We generally recommend generally that the is used for launching multiple instances of a particular type of analysis. Using this option, jobs launched are run sequentially. If you have been running multiple RNA-Seq analyses simultaneously on an affected Workbench, and you are not able to upgrade immediately, then on your current Workbench, re-run the RNA-Seq Analysis tasks sequentially.
Symptoms of this issue One or more of the concurrently run RNA-Seq Analysis tasks fails with an error. Currently we are aware of three possible error messages being associated with this issue: 'Index out of bounds', IllegalArgumentException' and 'Modifying call after finished not supported'. Some concurrently run RNA-Seq Analysis tasks that have EM turned on may succeed, but these may include incorrect results. Failure and incomplete imports for gzip and bzip2 compressed Illumina and Ion Torrent files The issue described below has been fixed for CLC Genomics Workbench 9.5.1, Biomedical Genomics Workbench 3.5.1 and CLC Genomics Server 8.5.1. If you are running the CLC Genomics Workbench 9.5, Biomedical Genomics Workbench 3.5 or CLC Genomics Server 8.5, please update your installation. Description of the issue The problems in the list below can arise when using the tools Import Illumina and Import Ion Torrent to import fastq files compressed with gzip (.gzip) or bzip2 (.bz2).
The problems are expected to be seen most frequently on Windows systems, but can sometimes also arise on Mac or Linux. The software affected is CLC Genomics Workbench 9.5, Biomedical Genomics Workbench 3.5 and CLC Genomics Server 8.5. Import can fail with an error message 'Errors occurred: see log'. No sequences are imported. The failure is sporadic: sometimes an import will succeed, but other times it will not. Import may seem to succeed, when in fact only a subset of the sequences in the fastq file(s) are imported.
Workaround if upgrading immediately is not an option If you are running one of the affected software versions, we recommend that you upgrade your software as soon as possible. However, if you cannot do that immediately, a work-around to this issue is to decompress the sequence files before importing them. Software affected by this problem. Biomedical Genomics Workbench 3.5. CLC Genomics Workbench 9.5. CLC Genomics Server 8.5 Other versions of these products are not affected. Genes with transcripts and with identical names reported as having 0 counts even with mapped reads The issue When running the RNA-Seq tool using track based references and.
using the option 'Genomes annotated with genes and transcripts', and. two or more genes had the same name, and.
a transcript could be assigned to each of these genes from the mRNA track then the value in the 'Transcripts annotated' column in the GE track and in the TE track was 0, and all counts for such genes were reported as zero, even when there were reads mapping to them. Which software and versions are affected? This issue affects:. CLC Genomics Workbench 9.0, 8.0 through 8.5.2, and 7.0 through 7.5.5. Biomedical Genomics Workbench 3.0, and 2.1 through 2.5.2.
CLC Cancer Research Workbench 1.0 through 2.0. CLC Genomics Server 8.0, 7.0 through 7.5.2, and 6.0 through 6.5.6 Which software versions are fixed?
This issue is fixed in the CLC Genomics Workbench 9.0.1, Biomedical Genomics Workbench 3.0.1 and CLC Genomics Server 8.0.1, released on June 9, 2016. It has also been addressed in the previous release line: CLC Genomics Workbench 8.5.3, Biomedical Genomics Workbench 2.5.3, and CLC Genomics Server 7.5.3, released June 16, 2016. The release notes describing the fix for this issue can be found on the pages for each product.
This particular fix is described as follows: Fixed an issue with the RNA-Seq Analysis tool that could arise when the 'Genomes annotated with genes and transcripts' option was chosen: If two or more genes had the same name, and a transcript could be assigned to each from the mRNA track, then the value in the 'Transcripts annotated' column in the GE track and in the TE track was 0. Furthermore, all counts for such genes were reported as zero, even when there were reads mapping to them. How can I check if my RNA-Seq Analysis has been affected by the issue? To find out if your analysis is affected you:.
Sort the TE track table on the column: 'Transcripts annotated'. Any transcripts that have 0 in this column are affected. All other transcripts are not affected by this bug. The bug was present at a very late stage in the RNA-Seq algorithm execution, when the calculation results were entered into the table. The underlying calculations were done correctly, but values for the duplicated gene names were excluded. The nonzero values that made it into the table are correct and will not change with the fix. While transcripts with 0 in the 'Transcripts annotated' column (affected transcripts) will often be seen when using the affected software versions under the analysis conditions described above, we do not anticipate that it will be necessary to re-run analyses in most cases.
Only a very small number of genes/transcripts would generally be affected and these may not be genes of interest to the analysis. For example, in many cases, genes given the same name code for rRNAs, snoRNA, and other miscellaneous RNAs, rather than mRNAs. If you do see affected transcripts associated with genes of potential interest, then we recommend re-running the analysis using a version of the software that includes a fix for this problem. Error in bed format file output for non-continous annotations Who is affected Users, who have exported annotation information to BED format from the below Workbench versions and where annotations consist of so-called block list entries (e.g.a mRNA made of of multiple exons).
Export of continuous annotations (e.g. Genes of prokaryotes) are not affected. CLC Genomics Workbench 8.5.1 and earlier.
CLC Cancer Research Workbench 2.0 and earlier. Biomedical Genomics Workbench 2.5.1 and earlier. CLC Genomics Server 7.5.1 and earlier What are the symptoms The 12th column of the exported BED file, 'blockStarts', according to the BED format should report the starting position of each 'block' of a feature (e.g. The individual exons) relatively to the start of the feature as reported in the 'chromStart'column.
The blockStarts column instead mistakenly gives the absolute genomics sequence coordinates for the start of exons. Re-import of the BED file into the Workbench or import into alternate programs, will produce distorted annotation information. When will this be fixed This issue was fixed in the following versions, released in March, 2016:. CLC Genomics Workbench 9.0.
Biomedical Genomics Workbench 3.0. CLC Genomics Server 3.0 3.8. Read Mapping Global alignment setting resulting in too many unmapped reads (multiple tools) Who is affected For all the below mentioned affected tools, this issue is relevant only if the parameter Global alignment has been selected. Note that this is not the default setting. Users will need to specifically have checked the Global alignment option for results to be affected by this issue. What are the symptoms. The number of mapped reads is substantially lower that what is expected or what was seen with previous Workbench versions.
For paired read sets, the number of broken reads will be significantly higher than expected (as one of the mates will by mistake not be mapped).