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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

Download Custom Microbial Reference Database – “One per genus” option may produce erroneous genome selection

CLC Network License Manager 5.5.2 temporarily and occasionally fails to serve network licenses

Authentication of upload to QCI Interpret servers in Turkey and Japan through browser fails

Two reference insertion variants can be reported at the same position


Issues affecting only older versions of products

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