• Product manuals

Browse the manual

• Introduction
  • The concept of CLC Haplotype Calling
  • Contact information
  • System requirements and installation
    • System requirements
    • Installation of plugins
    • Uninstalling plugins
  • Reference data management
    • The Reference Data Manager
• Data import
  • Import
    • VCF
    • Standard CLC Variant Track
• Data export
  • Export Genotype Track as VCF
  • Export Allele Table as CSV
  • Export Marker Genotypes as CSV or TSV
• Genotype Track
  • Genome Model
  • Locus Table
  • Allele Table
  • Header View
  • Track View
• Microhaplotype Caller
  • Microhaplotype Caller - Method
  • Microhaplotype Caller - Options
  • Microhaplotype Caller - Filters
    • General filters
    • Detection filters
    • Noise filters
  • Microhaplotype Caller - Annotations
• Glossary
  • Glossary
• Human Identity workflows
  • Detect QIAseq Human Indentity SNPs and Microhaplotypes
• Bibliography

Track View

The Track view of the Genotype track has the following options in the Track layout side panel:

Data aggregation

Allows you to specify whether the information in the track should be shown in detail or whether you wish to aggregate data. By aggregating data you decrease the detail level but increase the speed of the data display process, which is of particular interest when working with big data sets. The threshold (in bp) for when data should be aggregated can be specified with the drop-down box. The threshold describes the unit (or "bucket") size in base pairs, above which the data will start being aggregated. The bucket size depends on the track length and the zoom level. Hence, a data aggregation threshold with a low value will only show details when zoomed in, whereas a high value means that you can see details even when zoomed out. Please note that when using the high values, it will take longer time to display the data on the screen.

Show filtered

When enabled, alleles with applicable filters will be shown crossed out. Filtered alleles are hidden as default.

Reference alleles

Show reference alleles in a dimmed color to make them more distinguishable.

View mode

The view mode selection specifies whether the multiplicity of the displayed allele is based on its allele count in the sample (see 'Allele count' annotation in allele table), or on the number of haplotypes it is part of. An allele may be part of multiple haplotypes describing different aspects of the same DNA molecule (see 'Haplotypes' annotation in allele table).

• Allele count For each locus the alleles are displayed according to their allele count in the sample. Haplotype details are not available in this view mode.
• Haplotypes Haplotypes are displayed as linked haplotype alleles. Annotation and filter details are available in the tooltip when hovering over a haplotype allele. If the haplotypes are not separate (see 'Separation' annotation in allele table) they may describe the same DNA molecule in the sample genome.

Annotation color

Makes it possible to change the allele color.

---