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• Introduction
  • Contact information
  • System requirements
  • Installing modules
    • Licensing modules
    • Uninstalling modules
  • Installing server extensions
    • Licensing server extensions
• Methods and tools
  • Methods
    • Trimming
    • Readmapping
    • Deduplication
    • Local realignment
    • Structural variant detection
    • UMI grouping
    • Germline variant detection
    • Somatic variant detection
    • Tumor normal variant detection
    • Limitations
  • Tools
    • LightSpeed Fastq to Germline Variants
      • LightSpeed Fastq to Germline Variants outputs
    • LightSpeed Fastq to Somatic Variants
      • LightSpeed Fastq to Somatic Variants outputs
    • LightSpeed Fastq to Somatic Variants Tumor Normal
      • LightSpeed Fastq to Somatic Variants Tumor Normal outputs
    • Report
• Template Workflows
  • General Template Workflows
    • Fastq to Annotated Germline Variants
      • Outputs from Fastq to Annotated Germline Variants
    • Fastq to Annotated Germline Variants with Coverage Analysis
      • Outputs from Fastq to Annotated Germline Variants with Coverage Analysis
    • Fastq to Annotated Somatic Variants
      • Outputs from Fastq to Annotated Somatic Variants
    • Fastq to Annotated Somatic Variants with Coverage Analysis
      • Outputs from Fastq to Annotated Somatic Variants with Coverage Analysis
    • Fastq to Annotated Somatic Variants (Tumor Normal)
      • Outputs from Fastq to Annotated Somatic Variants (Tumor Normal)
    • Fastq to Annotated Somatic Variants (Tumor Normal) with Coverage Analysis
      • Outputs from Fastq to Annotated Somatic Variants (Tumor Normal) with Coverage Analysis
    • Fastq to Germline CNV Control
      • Outputs from Fastq to Germline CNV Control
    • Fastq to Somatic CNV Control
      • Outputs from Fastq to Somatic CNV Control
  • Template Workflows - QIAseq Targeted DNA
    • QIAseq Fastq to Annotated Germline Variants
      • Outputs from QIAseq Fastq to Annotated Germline Variants
    • QIAseq Fastq to Annotated Somatic Variants
      • Outputs from QIAseq Fastq to Annotated Somatic Variants
    • QIAseq Fastq to Germline CNV Control
      • Outputs from QIAseq Fastq to Germline CNV Control
    • QIAseq Fastq to Somatic CNV Control
      • Outputs from QIAseq Fastq to Somatic CNV Control
  • Template Workflows - QIAseq Targeted DNA Pro
    • QIAseq Pro Fastq to Annotated Germline Variants
      • Outputs from QIAseq Pro Fastq to Annotated Germline Variants
    • QIAseq Pro Fastq to Annotated Somatic Variants
      • Outputs from QIAseq Pro Fastq to Annotated Somatic Variants
    • QIAseq Pro Fastq to Germline CNV Control
      • Outputs from QIAseq Pro Fastq to Germline CNV Control
    • QIAseq Pro Fastq to Somatic CNV Control
      • Outputs from QIAseq Pro Fastq to Somatic CNV Control

Somatic variant detection

Based on the read mapping, somatic variants are identified at positions where the read alignment supports a significant difference to the reference genome. This is achieved by a significance assessment relative to the global error rate which is supplemented by a significance assessment relative to the local error rate as estimated from the data in the local vicinity of the variant. Furthermore, variants are assessed for strand imbalance significance and an additional assessment of significance of variants in low complexity contexts.

In contrast to the germline variant caller (Germline variant detection), the somatic variant caller makes no assumptions about the ploidy of a sample, and thus allows for sensitive detection of variant alleles at any, and low, frequencies.

Variant types

LightSpeed Fastq to Somatic Variants reports SNPs, MNVs and InDels and replacements provided that the variants are contained within at least one paired end read.

Variant annotations

Variants identified by LightSpeed Fastq to Somatic Variants are annotated with the following basic information: Chromosome, Region, Type, Reference, Allele, Reference allele, Length, Zygosity, Count, Coverage, Frequency, Forward read count, Reverse read count, Forward read coverage, Reverse read coverage, Forward/reverse balance and Genotype.

Read more about these general variant annotations here: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Variant_tracks.html.

In addition, the following LightSpeed specific annotations are available:

• p-value - global error rate p-value from binomial test given count, coverage and an error rate of 0.005. Note that if UMIs are utilized, i.e., in the UMI step a UMI preset has been selected or a custom read structure with UMIs has been specified (see LightSpeed Fastq to Somatic Variants), an error rate of 0.004 is used.
• p-value - global error rate (phred scaled) Log transformed p-value - global error rate.
• p-value - local error rate The minimum p-value from two individual tests: 1. A binomial test given forward count, forward coverage and a local error rate for forward reads estimated from the data. 2. A binomial test given reverse count, reverse coverage and a local error rate for reverse reads estimated from the data.
• p-value - low complexity p-value from binomial test given count and coverage. This p-value is only calculated for variants that are located in positions where two upstream and two downstream reference symbols are identical to the variant. For sites not living up to this criteria, a p-value of 0 is reported.
• Strand balance score 1 - (p-value from binomial test given forward count, count, and forward count/coverage).
• Inferred from unaligned ends Yes/no annotation indicating if the variant is a tandem duplication inferred from unaligned ends during detection of structural variants.
• Subtype Annotation indicating that an insertion is a tandem duplication. This annotation is added to tandem duplications inferred from unaligned ends during detection of structural variants, but also to insertions called by the standard variant caller that perfectly match a tandem duplication called during structural variant detection.
• Nearby similar called variant Annotation indicating if tandem duplications inferred from unaligned ends during structural variant detection resemble, but are not identical to an insertion called by the standard somatic variant detection.

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