Haplotype Calling

The Haplotype Calling (beta) plugin contains tools and tracks that support haplotype-aware variant detection, VCF import and export of variants annotated with phasing information and a workflow for the analysis of QIAseq Human Identity panel data.

Variant detection

The plugin contains the Microhaplotype Caller, which detects genomic variants and annotates them with read-based phasing information. The tool outputs variants in a new object called a Genotype track.

It is possible to pre-define marker loci for which genotypes should always be reported, allowing for genotyping homozygous reference alleles.

Variant representation

The Genotype track represents variants at both allele and locus levels. The Genotype track Allele table resembles traditional variant tables by displaying individual variants on separate rows. In contrast, the Locus table reports all variants for a given locus in a single row and summarizes called alleles in a Genotype annotation.

Variant phasing can be visualized in a genome browser view, where phased variants are connected by a vertical line.

Figure 1. Screenshot of two phased variants in a genome browser view and the corresponding locus table.

Variant filtering

As default, the Genotype track displays variants that have passed variant calling filter criteria, but variants that do not pass filter criteria are also retained in the track. These are easily inspected by enabling “Show filtered” in Table Settings.

Figure 2. Screenshot of a locus table where a variant that has been filtered based on coverage is shown when “Show filtered” is enabled. The “Locus filter” column lists filter criteria that have not been met.

Support for Human Identification (HID) panels

The Microhaplotype Caller is intended to be used with the Detect QIAseq Human Identity SNPs and Microhaplotypes (beta) workflow.

The workflow supports variant detection in target regions and provides genotypes for a specified set of markers.

VCF import and export

VCF files can be imported to a Genotype track, and variants in a Genotype track can be exported to VCF format. For both import and export, phasing information is retained. Filtered variants are included in the VCF file with the annotation given in the “Locus filter” column of the Genotype track locus table.

Known limitations

• These tools are optimized for working with data from smaller panels. They are not designed for handling the whole human genome or whole exome sequencing data.
• The Biomedical Genomics Analysis plugin 21.0 must be installed for running the workflow ‘Detect QIAseq Human Identity SNPs and Microhaplotypes (beta)’.