Important QIAGEN CLC software notifications

The QIAGEN Digital Insights Support and R&D teams are constantly reviewing support tickets and bug reports so any known issue can be handled and is fixed as soon as possible. Our aim is to ensure that QIAGEN CLC software maintains the highest possible quality to make your research faster, better and easier. Below is a list of known issues with suggested workarounds.

Issues affecting latest releases of products

Two reference insertion variants can be reported at the same position
 

Issues affecting only older versions of products

Create UMI Reads from Reads cannot group read pairs when R1 or R2 reads have different start positions
Find Resistance with ShortBRED is unable to detect short AMR markers
Analysis of xHYB QIAseq Viral Panel Data - targeted genomes may go undetected due to reference data issue
Find Resistance with PointFinder can report a resistance-causing insertion when the variant supported by the reads is different
Taxonomic Profiling sequence list outputs only include reads from the first sequence list input
Maximum Likelihood Phylogeny for protein alignments produces sub-optimal trees for some substitution models
CLC Network License Manager 5.5.2 temporarily and occasionally fails to serve network licenses
UHGG database for taxonomic profiling contains sequences with long unintentional stretches of N's
Download Custom Microbial Reference Database - "One per genus" option may produce erroneous genome selection
Copy Number Variant Detection (CNVs) can give wrong results when targets overlap and coverage tables are used as controls
PointFinder databases contain incorrect insertions and deletions
QIAseq xHYB Viral Panels reference data set v1.2 - Respiratory reference database element contains different SARS-Cov sub-species than listed in panel target list
Differential Abundance Analysis may use wrong values for samples with multiple metadata associations
Broken reads and ambiguously mapped reads are included in LightSpeed variant count and coverage values
Find Best References Using Read Mapping uses only first References and Host references inputs
IVA plugin and upload of variants following retirement of Ingenuity Variant Analysis (IVA)
QIAGEN RNA-seq Analysis Portal – Differential expression fold change values for All group pairs comparisons may be the opposite direction to that intended
ClinVar from the June 22, 2022 update of CLC reference data is incomplete
Local Realignment can introduce false positive insertions and deletions
QIAGEN RNA-seq Analysis Portal – miRNA expression value downloads may give wrong CPM value
Region and gene-level CNV detection problems when low coverage control targets present
Download Pathogen Database returns too few reference sequences
Transmembrane Helix Prediction always reports no transmembrane regions found
Housekeeping gene normalization is never applied by the tool Differential Expression in Two Groups
Error message appears when Primer info settings are enabled
Metadata layers are displayed incorrectly on results produced by the tool Create Heat Map for RNA-Seq
Error message when working with custom view settings with additional restriction enzymes
Mean reference gene coverage value in QC for RNAScan Panels report is too high
Updated values of unlocked parameters in Filter using Custom Criteria not used in first run of workflow
Extract Reads from Selection in abundance tables not working as expected in some circumstances
Taxonomic Profiling accepts multiple host index files but uses only the first one
Taxonomic Profiling reports too few reads in low complexity samples
Import of COSMIC Release v90 is not supported
Restrictions on sequence names when creating BLAST databases
Incorrect annotation and visualization of a small minority of overlapping variants
False positives and misannotation of some fusions in fusion detection workflows
Expression values from UPX 3' Transcriptome Kit data are systematically too high in many cases
Create MLST Scheme tool leads to strains being linked to wrong sequence type in some cases
Incorrect ARO numbers on some ResFinder entries in QMI-AR databases
Bonferroni and FDR multiple testing corrections too strict for differential expression analyses
Local realignment of certain UMI reads may differ between runs
Sporadic corruption of analysis outputs on GPFS file systems
Variants that span a target region are not called
Variants covering the exact length of a target region are not called and variants are not called for target regions of 1bp
Interquartile range test of the Detect MSI Status tool reports all loci as unstable
Reference multi-nucleotide variants (MNVs) are removed when applying filter or annotation tools under some circumstances
Loss of reference allele information for neighboring SNPs when using certain downstream filtering tools after variant calling
Some larger single deletions reported as multiple, individual deletions when affine gap scoring used
RNA-Seq Analysis does not count some reads covering start-end position of a circular chromosome
QIAseq Mitochondria Panel DHS-105Z workflow analyses use incorrect genetic code
Sample to Insight
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